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

Packages that use Alias

Package	Description
psidev.psi.mi.jami.binary.impl
psidev.psi.mi.jami.bridges.ols
psidev.psi.mi.jami.enricher.impl.full
psidev.psi.mi.jami.enricher.impl.minimal
psidev.psi.mi.jami.enricher.listener.impl
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.enricher.util
psidev.psi.mi.jami.listener
psidev.psi.mi.jami.listener.impl
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.tab.io.writer.feeder
psidev.psi.mi.jami.tab.io.writer.feeder.extended
psidev.psi.mi.jami.tab.utils
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.comparator
psidev.psi.mi.jami.utils.comparator.alias
psidev.psi.mi.jami.utils.comparator.interactor
psidev.psi.mi.jami.xml.io.writer.elements
psidev.psi.mi.jami.xml.io.writer.elements.impl
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30
psidev.psi.mi.jami.xml.model.extension
psidev.psi.mi.jami.xml.model.extension.binary
psidev.psi.mi.jami.xml.model.extension.binary.xml30
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300
psidev.psi.mi.jami.xml.model.reference
psidev.psi.mi.jami.xml.model.reference.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300
psidev.psi.mi.jami.xml.utils

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

Methods in psidev.psi.mi.jami.binary.impl that return types with arguments of type Alias

Modifier and Type	Method	Description
Collection<Alias>	DefaultNamedBinaryInteraction.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultNamedBinaryInteractionEvidence.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultNamedModelledBinaryInteraction.getAliases()	Getter for the field aliases.

Method parameters in psidev.psi.mi.jami.binary.impl with type arguments of type Alias

Modifier and Type	Method	Description
protected void	DefaultNamedBinaryInteraction.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultNamedBinaryInteractionEvidence.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultNamedModelledBinaryInteraction.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith

Uses of Alias in psidev.psi.mi.jami.bridges.ols

Methods in psidev.psi.mi.jami.bridges.ols that return types with arguments of type Alias

Modifier and Type	Method	Description
Collection<Alias>	LazyCvTerm.getSynonyms()	getSynonyms.

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

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

Modifier and Type	Method	Description
void	FullFeatureEvidenceEnricher.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FullFeatureEvidenceUpdater.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FullFeatureUpdater.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FullFeatureEvidenceEnricher.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FullFeatureEvidenceUpdater.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FullFeatureUpdater.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.

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

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

Modifier and Type	Method	Description
void	MinimalFeatureEnricher.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	MinimalFeatureEvidenceUpdater.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	MinimalFeatureEnricher.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	MinimalFeatureEvidenceUpdater.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.

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

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

Modifier and Type	Method	Description
void	ComplexEnricherListenerManager.onAddedAlias(Complex o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	CvTermEnricherListenerManager.onAddedAlias(CvTerm cv, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FeatureEnricherListenerManager.onAddedAlias(T o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	InteractorEnricherListenerManager.onAddedAlias(T interactor, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	OrganismEnricherListenerManager.onAddedAlias(Organism organism, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	ParticipantEnricherListenerManager.onAddedAlias(P o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	ComplexEnricherListenerManager.onRemovedAlias(Complex o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	CvTermEnricherListenerManager.onRemovedAlias(CvTerm o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FeatureEnricherListenerManager.onRemovedAlias(T o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	InteractorEnricherListenerManager.onRemovedAlias(T interactor, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	OrganismEnricherListenerManager.onRemovedAlias(Organism organism, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	ParticipantEnricherListenerManager.onRemovedAlias(P o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.

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

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

Modifier and Type	Method	Description
void	ComplexEnricherStatisticsWriter.onAddedAlias(Complex o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	CvTermEnricherStatisticsWriter.onAddedAlias(CvTerm cv, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FeatureEnricherStatisticsWriter.onAddedAlias(T o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	InteractorEnricherStatisticsWriter.onAddedAlias(T interactor, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	OrganismEnricherStatisticsWriter.onAddedAlias(Organism organism, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	ParticipantEnricherStatisticsWriter.onAddedAlias(P o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	ComplexEnricherStatisticsWriter.onRemovedAlias(Complex o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	CvTermEnricherStatisticsWriter.onRemovedAlias(CvTerm cv, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FeatureEnricherStatisticsWriter.onRemovedAlias(T o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	InteractorEnricherStatisticsWriter.onRemovedAlias(T interactor, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	OrganismEnricherStatisticsWriter.onRemovedAlias(Organism organism, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	ParticipantEnricherStatisticsWriter.onRemovedAlias(P o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.

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

Method parameters in psidev.psi.mi.jami.enricher.util with type arguments of type Alias

Modifier and Type	Method	Description
static <T> void	EnricherUtils.mergeAliases(T termToEnrich, Collection<Alias> toEnrichAliases, Collection<Alias> fetchedAliases, boolean remove, AliasesChangeListener<T> aliasListener)	mergeAliases.

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

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

Modifier and Type	Method	Description
void	AliasesChangeListener.onAddedAlias(T o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	AliasesChangeListener.onRemovedAlias(T o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.

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

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

Modifier and Type	Method	Description
void	CvTermChangeLogger.onAddedAlias(CvTerm cv, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FeatureChangeLogger.onAddedAlias(T protein, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	InteractorChangeLogger.onAddedAlias(T protein, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	OrganismChangeLogger.onAddedAlias(Organism organism, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	ParticipantChangeLogger.onAddedAlias(T protein, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	CvTermChangeLogger.onRemovedAlias(CvTerm cv, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FeatureChangeLogger.onRemovedAlias(T protein, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	InteractorChangeLogger.onRemovedAlias(T protein, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	OrganismChangeLogger.onRemovedAlias(Organism organism, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	ParticipantChangeLogger.onRemovedAlias(T protein, Alias removed)	Listen to the event where an alias has been removed from the object aliases.

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

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

Modifier and Type	Method	Description
<A extends Alias> Collection<A>	Feature.getAliases()	Collection of aliases for a feature.
<A extends Alias> Collection<A>	Interactor.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
<A extends Alias> Collection<A>	NamedExperiment.getAliases()	Collection of aliases for an experiment.
<A extends Alias> Collection<A>	NamedInteraction.getAliases()	Collection of aliases for an interaction.
<A extends Alias> Collection<A>	Organism.getAliases()	The other names of the organism.
<A extends Alias> Collection<A>	Participant.getAliases()	Collection of aliases which give more information about the participant.
<A extends Alias> Collection<A>	CvTerm.getSynonyms()	Collection of synonyms for this CvTerm This method should never return null.

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

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

Modifier and Type	Class	Description
class	DefaultAlias	Default implementation of Alias.

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

Modifier and Type	Method	Description
Collection<Alias>	AbstractFeature.getAliases()	Getter for the field aliases.
Collection<Alias>	AbstractParticipant.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultComplex.getAliases()	getAliases
Collection<Alias>	DefaultInteractor.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultNamedExperiment.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultNamedInteraction.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultNamedInteractionEvidence.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultNamedModelledInteraction.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultOrganism.getAliases()	Getter for the field aliases.
Collection<Alias>	DefaultCvTerm.getSynonyms()	Getter for the field synonyms.

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

Modifier and Type	Method	Description
protected void	DefaultComplex.processAddedAliasEvent(Alias added)	processAddedAliasEvent
protected void	DefaultProtein.processAddedAliasEvent(Alias added)	processAddedAliasEvent
protected void	DefaultComplex.processRemovedAliasEvent(Alias removed)	processRemovedAliasEvent
protected void	DefaultProtein.processRemovedAliasEvent(Alias removed)	processRemovedAliasEvent

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

Modifier and Type	Method	Description
protected void	AbstractFeature.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	AbstractParticipant.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultInteractor.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultNamedExperiment.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultNamedInteraction.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultNamedInteractionEvidence.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultNamedModelledInteraction.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultOrganism.initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	DefaultCvTerm.initialiseSynonymsWith(Collection<Alias> aliases)	initialiseSynonymsWith

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

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

Modifier and Type	Class	Description
class	MitabAlias	Extended alias in MITAB

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

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

Modifier and Type	Method	Description
void	AbstractMitabColumnFeeder.writeAlias(Alias alias)	This methods write the dbsource, alias name and alias type of an alias
void	DefaultMitabColumnFeeder.writeAlias(Participant participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	MitabColumnFeeder.writeAlias(P participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	MitabColumnFeeder.writeAlias(Alias alias)	This methods write the dbsource, alias name and alias type of an alias
void	MitabInteractionEvidenceFeeder.writeAlias(ParticipantEvidence participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	MitabModelledInteractionFeeder.writeAlias(ModelledParticipant participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.

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

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

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

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

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

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

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

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

Modifier and Type	Method	Description
static Alias	AliasUtils.collectFirstAliasWithType(Collection<? extends Alias> aliases, String typeId, String typeName)	This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name
static Alias	AliasUtils.collectFirstAliasWithTypeAndName(Collection<? extends Alias> aliases, String typeId, String typeName, String name)	This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name
static Alias	AliasUtils.createAlias(String typeName, String name)	createAlias
static Alias	AliasUtils.createAlias(String typeName, String typeMi, String name)	createAlias
static Alias	AliasUtils.createAuthorAssignedName(String name)	createAuthorAssignedName
static Alias	AliasUtils.createComplexSynonym(String name)	createComplexSynonym
static Alias	AliasUtils.createGeneName(String name)	createGeneName
static Alias	AliasUtils.createGeneNameSynonym(String name)	createGeneNameSynonym
static Alias	AliasUtils.createIsoformSynonym(String name)	createIsoformSynonym
static Alias	AliasUtils.createLocusName(String name)	createLocusName
static Alias	AliasUtils.createOrfName(String name)	createOrfName

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

Modifier and Type	Method	Description
static Collection<Alias>	AliasUtils.collectAllAliasesHavingType(Collection<? extends Alias> aliases, String typeId, String typeName)	Extract all the aliases having a specific type.
static Collection<Alias>	AliasUtils.collectAllAliasesHavingTypeAndName(Collection<? extends Alias> aliases, String typeId, String typeName, String name)	Extract all the aliases having a specific type.

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

Modifier and Type	Method	Description
static boolean	AliasUtils.doesAliasHaveType(Alias alias, String typeId, String typeName)	To know if an alias have a specific type.
static boolean	AliasUtils.doesAliasHaveTypeAndName(Alias alias, String typeId, String typeName, String name)	To know if an alias have a specific type and name.

Method parameters in psidev.psi.mi.jami.utils with type arguments of type Alias

Modifier and Type	Method	Description
static Collection<Alias>	AliasUtils.collectAllAliasesHavingType(Collection<? extends Alias> aliases, String typeId, String typeName)	Extract all the aliases having a specific type.
static Collection<Alias>	AliasUtils.collectAllAliasesHavingTypeAndName(Collection<? extends Alias> aliases, String typeId, String typeName, String name)	Extract all the aliases having a specific type.
static Alias	AliasUtils.collectFirstAliasWithType(Collection<? extends Alias> aliases, String typeId, String typeName)	This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name
static Alias	AliasUtils.collectFirstAliasWithTypeAndName(Collection<? extends Alias> aliases, String typeId, String typeName, String name)	This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name
static void	AliasUtils.removeAllAliasesWithType(Collection<? extends Alias> aliases, String typeId, String typeName)	Remove all Alias having this method name/method id from the collection of aliases
static void	AliasUtils.removeAllAliasesWithTypeAndName(Collection<Alias> aliases, String typeId, String typeName, String name)	Remove all Alias having this method name/method id from the collection of aliases

Uses of Alias in psidev.psi.mi.jami.utils.comparator

Method parameters in psidev.psi.mi.jami.utils.comparator with type arguments of type Alias

Modifier and Type	Method	Description
static boolean	ComparatorUtils.findAtLeastOneMatchingAlias(Collection<? extends Alias> aliases1, Collection<? extends Alias> aliases2)	findAtLeastOneMatchingAlias

Uses of Alias in psidev.psi.mi.jami.utils.comparator.alias

Methods in psidev.psi.mi.jami.utils.comparator.alias with parameters of type Alias

Modifier and Type	Method	Description
static boolean	DefaultAliasComparator.areEquals(Alias alias1, Alias alias2)	Use DefaultAliasComparator to know if two aliases are equals.
static boolean	UnambiguousAliasComparator.areEquals(Alias alias1, Alias alias2)	Use UnambiguousAliasComparator to know if two aliases are equals.
int	AliasComparator.compare(Alias alias1, Alias alias2)	It will first compare alias types and then alias names (case sensitive) - Two aliases which are null are equals - The alias which is not null is before null.
int	UnambiguousAliasComparator.compare(Alias alias1, Alias alias2)	It will first compare alias types and then alias names (case sensitive) - Two aliases which are null are equals - The alias which is not null is before null.
static int	UnambiguousAliasComparator.hashCode(Alias alias)	hashCode

Uses of Alias in psidev.psi.mi.jami.utils.comparator.interactor

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

Modifier and Type	Method	Description
CollectionComparator<Alias>	InteractorBaseComparator.getAliasCollectionComparator()	Getter for the field aliasCollectionComparator.
Comparator<Alias>	InteractorBaseComparator.getAliasComparator()	Getter for the field aliasComparator.

Uses of Alias 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 Alias

Modifier and Type	Method	Description
static PsiXmlElementWriter<Alias>	PsiXmlElementWriterFactory.createAliasWriter(XMLStreamWriter streamWriter)	createAliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements with type arguments of type Alias

Modifier and Type	Method	Description
static PsiXmlVariableNameWriter<CvTerm>	PsiXmlElementWriterFactory.createCvWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlXrefWriter primaryRefWriter)	createCvWriter.
static PsiXmlInteractionWriter[]	PsiXmlElementWriterFactory.createDefaultPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createDefaultPsiXmlInteractionWriters.
static PsiXmlVariableNameWriter<CvTerm>	PsiXmlElementWriterFactory.createExperimentalCvWriter(XMLStreamWriter streamWriter, PsiXmlVersion version, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlXrefWriter primaryRefWriter)	createExperimentalCvWriter.
static PsiXmlExperimentWriter	PsiXmlElementWriterFactory.createExperimentWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, boolean named, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlElementWriter<Organism> nonExperimentalHostOrganismWriter, PsiXmlVariableNameWriter<CvTerm> detectionMethodWriter, PsiXmlElementWriter<Confidence> confidenceWriter)	createExperimentWriter.
static PsiXmlInteractionWriter[]	PsiXmlElementWriterFactory.createExtendedPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createExtendedPsiXmlInteractionWriters.
static <F extends Feature> PsiXmlElementWriter<F>[]	PsiXmlElementWriterFactory.createFeatureWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, InteractionCategory category, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVariableNameWriter<CvTerm> featureTypeWriter, PsiXmlParameterWriter parameterWriter)	createFeatureWriter.
static PsiXmlElementWriter<Organism>	PsiXmlElementWriterFactory.createHostOrganismWriter(XMLStreamWriter streamWriter, PsiXmlVersion version, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> annotationWriter, PsiXmlXrefWriter xrefWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createHostOrganismWriter.
static PsiXmlInteractionWriter[]	PsiXmlElementWriterFactory.createInteractionWritersFor(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, boolean extended, boolean named, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlElementWriter<Interactor> interactorWriter, PsiXmlPublicationWriter publicationWriter)	createInteractionWritersFor.
static PsiXmlElementWriter<Interactor>	PsiXmlElementWriterFactory.createInteractorWriter(PsiXmlVersion version, XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVariableNameWriter<CvTerm> interactorTypeWriter, PsiXmlElementWriter<Organism> organismWriter, PsiXmlElementWriter<Checksum> checksumWriter)	createInteractorWriter.
static PsiXmlInteractionWriter[]	PsiXmlElementWriterFactory.createNamedPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createNamedPsiXmlInteractionWriters.
static PsiXmlVariableNameWriter<CvTerm>	PsiXmlElementWriterFactory.createOpenCvWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter)	createOpenCvWriter.
static PsiXmlElementWriter<Organism>	PsiXmlElementWriterFactory.createOrganismWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> annotationWriter, PsiXmlXrefWriter xrefWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createOrganismWriter.
static <P extends Participant> PsiXmlParticipantWriter<P>[]	PsiXmlElementWriterFactory.createParticipantWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory category, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter<Confidence> confidenceWriter, PsiXmlElementWriter<Interactor> interactorWriter, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter, PsiXmlParameterWriter parameterWriter)	createParticipantWriter.
static PsiXmlSourceWriter	PsiXmlElementWriterFactory.createSourceWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlVersion version, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlPublicationWriter publicationWriter)	createSourceWriter.

Uses of Alias 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 Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	AbstractXmlSourceWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlCvTermWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlInteractorWriter.getAliasWriter()	Getter for the field aliasWriter.

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

Modifier and Type	Method	Description
void	XmlAliasWriter.write(Alias object)	write.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl with type arguments of type Alias

Modifier and Type	Method	Description
void	AbstractXmlSourceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlCvTermWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlInteractorWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

Uses of Alias 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 Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	AbstractXmlFeatureWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	AbstractXmlModelledInteractionWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	AbstractXmlOrganismWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	AbstractXmlParticipantWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with type arguments of type Alias

Modifier and Type	Method	Description
void	AbstractXmlFeatureWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	AbstractXmlModelledInteractionWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	AbstractXmlOrganismWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	AbstractXmlParticipantWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25 that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	XmlNamedBinaryInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedBinaryInteractionWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedInteractionWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25 with type arguments of type Alias

Modifier and Type	Method	Description
void	XmlNamedBinaryInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedBinaryInteractionWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedInteractionWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30 that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	XmlNamedBinaryInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30 with type arguments of type Alias

Modifier and Type	Method	Description
void	XmlNamedBinaryInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25 that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	XmlNamedBinaryInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedBinaryInteractionWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedInteractionWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25 with type arguments of type Alias

Modifier and Type	Method	Description
void	XmlNamedBinaryInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedBinaryInteractionWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedInteractionWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30 that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	XmlNamedBinaryInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Alias>	XmlNamedInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30 with type arguments of type Alias

Modifier and Type	Method	Description
void	XmlNamedBinaryInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	XmlNamedInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

Uses of Alias in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	AbstractXmlInteractionEvidenceWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended with type arguments of type Alias

Modifier and Type	Method	Description
void	AbstractXmlInteractionEvidenceWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

Uses of Alias in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25 that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	AbstractXmlInteractionWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25 with type arguments of type Alias

Modifier and Type	Method	Description
void	AbstractXmlInteractionWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25 that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	XmlNamedExperimentWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25 with type arguments of type Alias

Modifier and Type	Method	Description
void	XmlNamedExperimentWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 that return types with arguments of type Alias

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	XmlNamedExperimentWriter.getAliasWriter()	Getter for the field aliasWriter.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 with type arguments of type Alias

Modifier and Type	Method	Description
void	XmlNamedExperimentWriter.setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.

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

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

Modifier and Type	Method	Description
Collection<Alias>	AbstractBaseXmlInteractor.getAliases()	getAliases.
List<Alias>	AbstractNamesContainer.getAliases()	Gets the value of the alias property.
Collection<Alias>	ExtendedPsiXmlInteraction.getAliases()	getAliases.
Collection<Alias>	ExtendedPsiXmlInteractionEvidence.getAliases()	getAliases.
Collection<Alias>	ExtendedPsiXmlModelledInteraction.getAliases()	getAliases.
Collection<Alias>	PsiXmlInteraction.getAliases()	getAliases.

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

Modifier and Type	Method	Description
protected void	AbstractNamesContainer.initialiseAliasesWith(List<Alias> aliases)	initialiseAliasesWith.

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

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

Modifier and Type	Method	Description
List<Alias>	AbstractExtendedXmlBinaryInteraction.getAliases()	getAliases.
Collection<Alias>	AbstractXmlBinaryInteraction.getAliases()	getAliases.
Collection<Alias>	XmlBinaryInteractionEvidenceWrapper.getAliases()	getAliases.
Collection<Alias>	XmlBinaryInteractionWrapper.getAliases()	getAliases.
Collection<Alias>	XmlModelledBinaryInteractionWrapper.getAliases()	getAliases.

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

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

Modifier and Type	Method	Description
Collection<Alias>	XmlModelledBinaryInteraction.getAliases()	getAliases.
Collection<Alias>	XmlModelledBinaryInteractionWrapper.getAliases()	getAliases.

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

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

Modifier and Type	Class	Description
class	XmlAlias	Xml implementation of an Alias.

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

Modifier and Type	Method	Description
List<Alias>	AbstractXmlComplex.getAliases()	Collection of aliases for an interaction.
List<Alias>	AbstractXmlExperiment.getAliases()	Collection of aliases for an experiment.
List<Alias>	AbstractXmlFeature.getAliases()	Collection of aliases for a feature.
List<Alias>	AbstractXmlInteraction.getAliases()	Collection of aliases for an interaction.
List<Alias>	AbstractXmlParticipant.getAliases()	Collection of aliases which give more information about the participant.
Collection<Alias>	AbstractXmlParticipantPool.getAliases()	Collection of aliases which give more information about the participant.
List<Alias>	NamesContainer.getAliases()	Gets the value of the alias property.
Collection<Alias>	XmlBasicInteractionComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlFeatureEvidenceWrapper.getAliases()	Collection of aliases for a feature.
Collection<Alias>	XmlFeatureWrapper.getAliases()	Collection of aliases for a feature.
Collection<Alias>	XmlInteractionEvidenceComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlModelledInteractionComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlOrganism.getAliases()	getAliases.
Collection<Alias>	XmlParticipantEvidenceWrapper.getAliases()	Collection of aliases which give more information about the participant.
List<Alias>	XmlParticipantWrapper.getAliases()	Collection of aliases which give more information about the participant.
Collection<Alias>	AbstractXmlCvTerm.getSynonyms()	getSynonyms.

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

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

Modifier and Type	Class	Description
class	XmlAlias	Xml implementation of an Alias.

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

Modifier and Type	Method	Description
List<Alias>	AbstractXmlComplex.getAliases()	Collection of aliases for an interaction.
List<Alias>	AbstractXmlExperiment.getAliases()	Collection of aliases for an experiment.
List<Alias>	AbstractXmlFeature.getAliases()	Collection of aliases for a feature.
List<Alias>	AbstractXmlInteraction.getAliases()	Collection of aliases for an interaction.
List<Alias>	AbstractXmlParticipant.getAliases()	Collection of aliases which give more information about the participant.
Collection<Alias>	AbstractXmlParticipantPool.getAliases()	Collection of aliases which give more information about the participant.
List<Alias>	NamesContainer.getAliases()	Gets the value of the alias property.
Collection<Alias>	XmlBasicInteractionComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlFeatureEvidenceWrapper.getAliases()	Collection of aliases for a feature.
Collection<Alias>	XmlFeatureWrapper.getAliases()	Collection of aliases for a feature.
Collection<Alias>	XmlInteractionEvidenceComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlModelledInteractionComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlOrganism.getAliases()	getAliases.
Collection<Alias>	XmlParticipantEvidenceWrapper.getAliases()	Collection of aliases which give more information about the participant.
List<Alias>	XmlParticipantWrapper.getAliases()	Collection of aliases which give more information about the participant.
Collection<Alias>	AbstractXmlCvTerm.getSynonyms()	getSynonyms.

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

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

Modifier and Type	Class	Description
class	XmlAlias	Xml implementation of an Alias.

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

Modifier and Type	Method	Description
List<Alias>	AbstractXmlComplex.getAliases()	Collection of aliases for an interaction.
List<Alias>	AbstractXmlExperiment.getAliases()	Collection of aliases for an experiment.
List<Alias>	AbstractXmlFeature.getAliases()	Collection of aliases for a feature.
List<Alias>	AbstractXmlInteraction.getAliases()	Collection of aliases for an interaction.
List<Alias>	AbstractXmlParticipant.getAliases()	Collection of aliases which give more information about the participant.
Collection<Alias>	AbstractXmlParticipantPool.getAliases()	Collection of aliases which give more information about the participant.
Collection<Alias>	ExtendedPsiXmlModelledInteraction.getAliases()	getAliases.
List<Alias>	NamesContainer.getAliases()	Gets the value of the alias property.
Collection<Alias>	XmlBasicInteractionComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlFeatureEvidenceWrapper.getAliases()	Collection of aliases for a feature.
Collection<Alias>	XmlFeatureWrapper.getAliases()	Collection of aliases for a feature.
Collection<Alias>	XmlInteractionEvidenceComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
List<Alias>	XmlModelledInteraction.getAliases()	Collection of aliases for an interaction.
Collection<Alias>	XmlModelledInteractionComplexWrapper.getAliases()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Alias>	XmlOrganism.getAliases()	getAliases.
Collection<Alias>	XmlParticipantEvidenceWrapper.getAliases()	Collection of aliases which give more information about the participant.
List<Alias>	XmlParticipantWrapper.getAliases()	Collection of aliases which give more information about the participant.
Collection<Alias>	AbstractXmlCvTerm.getSynonyms()	getSynonyms.

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

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

Modifier and Type	Method	Description
Collection<Alias>	AbstractFeatureRef.getAliases()	Collection of aliases for a feature.

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

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

Modifier and Type	Method	Description
<A extends Alias> Collection<A>	AbstractExperimentRef.getAliases()	Collection of aliases for an experiment.

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

Modifier and Type	Method	Description
Collection<Alias>	AbstractComplexRef.getAliases()	getAliases.
Collection<Alias>	AbstractInteractorRef.getAliases()	getAliases.
Collection<Alias>	AbstractParticipantRef.getAliases()	getAliases.

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

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

Modifier and Type	Method	Description
<A extends Alias> Collection<A>	AbstractExperimentRef.getAliases()	Collection of aliases for an experiment.

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

Modifier and Type	Method	Description
Collection<Alias>	AbstractComplexRef.getAliases()	getAliases.
Collection<Alias>	AbstractInteractorRef.getAliases()	getAliases.
Collection<Alias>	AbstractParticipantRef.getAliases()	getAliases.

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

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

Modifier and Type	Method	Description
<A extends Alias> Collection<A>	AbstractExperimentRef.getAliases()	Collection of aliases for an experiment.

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

Modifier and Type	Method	Description
Collection<Alias>	AbstractComplexRef.getAliases()	getAliases.
Collection<Alias>	AbstractInteractorRef.getAliases()	getAliases.
Collection<Alias>	AbstractParticipantRef.getAliases()	getAliases.

Uses of Alias in psidev.psi.mi.jami.xml.utils

Method parameters in psidev.psi.mi.jami.xml.utils with type arguments of type Alias

Modifier and Type	Method	Description
static void	PsiXmlUtils.writeCompleteNamesElement(String shortLabel, String fullName, Collection<Alias> aliases, XMLStreamWriter writer, PsiXmlElementWriter<Alias> aliasWriter)	writeCompleteNamesElement.
static void	PsiXmlUtils.writeCompleteNamesElement(String shortLabel, String fullName, Collection<Alias> aliases, XMLStreamWriter writer, PsiXmlElementWriter<Alias> aliasWriter)	writeCompleteNamesElement.
static void	PsiXmlUtils.writeCompleteNamesForExperiment(NamedExperiment xmlExperiment, XMLStreamWriter writer, PsiXmlElementWriter<Alias> aliasWriter)	writeCompleteNamesForExperiment.