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

Packages that use Annotation

Package	Description
psidev.psi.mi.jami.binary.impl
psidev.psi.mi.jami.bridges.ols
psidev.psi.mi.jami.commons
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.json.elements
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.utils
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.comparator.annotation
psidev.psi.mi.jami.xml.io.writer
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.abstracts.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended
psidev.psi.mi.jami.xml.model
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.model.xml253
psidev.psi.mi.jami.xml.model.xml254
psidev.psi.mi.jami.xml.model.xml30
psidev.psi.mi.jami.xml.utils

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

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractBinaryInteractionWrapper.getAnnotations()	Getter for the field annotations.

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

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

Modifier and Type	Method	Description
Collection<Annotation>	LazyCvTerm.getAnnotations()	getAnnotations.

Methods in psidev.psi.mi.jami.bridges.ols with parameters of type Annotation

Modifier and Type	Method	Description
protected void	LazySource.processAddedAnnotationEvent(Annotation added)	processAddedAnnotationEvent.
protected void	LazySource.processRemovedAnnotationEvent(Annotation removed)	processRemovedAnnotationEvent.

Uses of Annotation in psidev.psi.mi.jami.commons

Method parameters in psidev.psi.mi.jami.commons with type arguments of type Annotation

Modifier and Type	Method	Description
Map<String,Object>	MIWriterOptionFactory.getCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, PsiXmlVersion version)	Create the options for the compact PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Experiment> experimentSet, Set<Interactor> interactorSet, Set<String> availabilitySet, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)	Create the options for the compact PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, PsiXmlVersion version)	Create the options for the expanded PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)	Create the options for the compact PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlType xmlType, PsiXmlObjectCache elementCache, Set<Experiment> experimentSet, Set<Interactor> interactorSet, Set<String> availabilitySet, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)	Create the options for the PSI-XML InteractionWriter.

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

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

Modifier and Type	Method	Description
void	FullFeatureEvidenceEnricher.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FullFeatureEvidenceUpdater.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FullFeatureUpdater.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FullFeatureEvidenceEnricher.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FullFeatureEvidenceUpdater.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FullFeatureUpdater.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.

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

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

Modifier and Type	Method	Description
void	MinimalFeatureEnricher.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	MinimalFeatureEvidenceUpdater.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	MinimalFeatureEnricher.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	MinimalFeatureEvidenceUpdater.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.

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

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

Modifier and Type	Method	Description
void	CvTermEnricherListenerManager.onAddedAnnotation(CvTerm o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ExperimentEnricherListenerManager.onAddedAnnotation(Experiment experiment, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FeatureEnricherListenerManager.onAddedAnnotation(T feature, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	InteractionEnricherListenerManager.onAddedAnnotation(I o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	InteractorEnricherListenerManager.onAddedAnnotation(T o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ParticipantEnricherListenerManager.onAddedAnnotation(P o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	PublicationEnricherListenerManager.onAddedAnnotation(Publication publication, Annotation annotationAdded)	Listen to the event where an annotation has been added to the object annotations.
void	CvTermEnricherListenerManager.onRemovedAnnotation(CvTerm o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ExperimentEnricherListenerManager.onRemovedAnnotation(Experiment experiment, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FeatureEnricherListenerManager.onRemovedAnnotation(T feature, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	InteractionEnricherListenerManager.onRemovedAnnotation(I o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	InteractorEnricherListenerManager.onRemovedAnnotation(T o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ParticipantEnricherListenerManager.onRemovedAnnotation(P o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	PublicationEnricherListenerManager.onRemovedAnnotation(Publication publication, Annotation annotationRemoved)	Listen to the event where an annotation has been removed from the object annotations.

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

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

Modifier and Type	Method	Description
void	CvTermEnricherStatisticsWriter.onAddedAnnotation(CvTerm o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ExperimentEnricherStatisticsWriter.onAddedAnnotation(Experiment o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FeatureEnricherStatisticsWriter.onAddedAnnotation(T feature, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	InteractionEnricherStatisticsWriter.onAddedAnnotation(I o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	InteractorEnricherStatisticsWriter.onAddedAnnotation(T o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ParticipantEnricherStatisticsWriter.onAddedAnnotation(P o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	PublicationEnricherStatisticsWriter.onAddedAnnotation(Publication publication, Annotation annotationAdded)	Listen to the event where an annotation has been added to the object annotations.
void	CvTermEnricherStatisticsWriter.onRemovedAnnotation(CvTerm o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ExperimentEnricherStatisticsWriter.onRemovedAnnotation(Experiment o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FeatureEnricherStatisticsWriter.onRemovedAnnotation(T feature, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	InteractionEnricherStatisticsWriter.onRemovedAnnotation(I o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	InteractorEnricherStatisticsWriter.onRemovedAnnotation(T o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ParticipantEnricherStatisticsWriter.onRemovedAnnotation(P o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	PublicationEnricherStatisticsWriter.onRemovedAnnotation(Publication publication, Annotation annotationRemoved)	Listen to the event where an annotation has been removed from the object annotations.

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

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

Modifier and Type	Method	Description
static <T> void	EnricherUtils.mergeAnnotations(T termToEnrich, Collection<Annotation> toEnrichAnnotations, Collection<Annotation> fetchedAnnotations, boolean remove, AnnotationsChangeListener<T> annotationListener)	mergeAnnotations.

Uses of Annotation in psidev.psi.mi.jami.json.elements

Methods in psidev.psi.mi.jami.json.elements that return types with arguments of type Annotation

Modifier and Type	Method	Description
JsonElementWriter<Annotation>	SimpleJsonExperimentWriter.getAnnotationWriter()	Getter for the field annotationWriter.

Methods in psidev.psi.mi.jami.json.elements with parameters of type Annotation

Modifier and Type	Method	Description
void	SimpleJsonAnnotationWriter.write(Annotation object)	write.

Method parameters in psidev.psi.mi.jami.json.elements with type arguments of type Annotation

Modifier and Type	Method	Description
void	SimpleJsonExperimentWriter.setAnnotationWriter(JsonElementWriter<Annotation> annotationWriter)	Setter for the field annotationWriter.
protected void	SimpleJsonExperimentWriter.writeAnnotations(Collection<Annotation> expModifications)	writeAnnotations.

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

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

Modifier and Type	Method	Description
void	AnnotationsChangeListener.onAddedAnnotation(T o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	AnnotationsChangeListener.onRemovedAnnotation(T o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.

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

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

Modifier and Type	Method	Description
void	CvTermChangeLogger.onAddedAnnotation(CvTerm cv, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ExperimentChangeLogger.onAddedAnnotation(Experiment experiment, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FeatureChangeLogger.onAddedAnnotation(T protein, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	InteractionChangeLogger.onAddedAnnotation(T interaction, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	InteractorChangeLogger.onAddedAnnotation(T protein, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ParticipantChangeLogger.onAddedAnnotation(T protein, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	PublicationChangeLogger.onAddedAnnotation(Publication publication, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	CvTermChangeLogger.onRemovedAnnotation(CvTerm cv, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ExperimentChangeLogger.onRemovedAnnotation(Experiment experiment, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FeatureChangeLogger.onRemovedAnnotation(T protein, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	InteractionChangeLogger.onRemovedAnnotation(T interaction, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	InteractorChangeLogger.onRemovedAnnotation(T protein, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ParticipantChangeLogger.onRemovedAnnotation(T protein, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	PublicationChangeLogger.onRemovedAnnotation(Publication publication, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.

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

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

Modifier and Type	Method	Description
<T extends Annotation> Collection<T>	CooperativeEffect.getAnnotations()	The Collection of annotations describing the cooperativeEffect.
<A extends Annotation> Collection<A>	CvTerm.getAnnotations()	Collection of annotations describing the CvTerm.
<A extends Annotation> Collection<A>	Experiment.getAnnotations()	Collection of annotations for an experiment.
<A extends Annotation> Collection<A>	Feature.getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
<A extends Annotation> Collection<A>	Interaction.getAnnotations()	The Collection of annotations describing the interaction.
<A extends Annotation> Collection<A>	Interactor.getAnnotations()	Collection of annotations for an interactor.
<A extends Annotation> Collection<A>	Participant.getAnnotations()	Collection of annotations describing the participant.
<A extends Annotation> Collection<A>	Publication.getAnnotations()	Other publication annotations which can give more information about the curated publication.

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

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

Modifier and Type	Class	Description
class	DefaultAnnotation	Default implementation for Annotation.

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractFeature.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	AbstractInteraction.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	AbstractParticipant.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	DefaultComplex.getAnnotations()	getAnnotations
Collection<Annotation>	DefaultCooperativeEffect.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	DefaultCvTerm.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	DefaultExperiment.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	DefaultInteractor.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	DefaultPublication.getAnnotations()	Getter for the field annotations.

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

Modifier and Type	Method	Description
protected void	DefaultComplex.processAddedAnnotationEvent(Annotation added)	processAddedAnnotationEvent
protected void	DefaultSource.processAddedAnnotationEvent(Annotation added)	processAddedAnnotationEvent
protected void	DefaultComplex.processRemovedAnnotationEvent(Annotation removed)	processRemovedAnnotationEvent
protected void	DefaultSource.processRemovedAnnotationEvent(Annotation removed)	processRemovedAnnotationEvent

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

Modifier and Type	Method	Description
protected void	AbstractFeature.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	AbstractInteraction.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	AbstractParticipant.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	DefaultCooperativeEffect.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	DefaultCvTerm.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	DefaultExperiment.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	DefaultInteractor.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	DefaultPublication.initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith

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

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

Modifier and Type	Class	Description
class	MitabAnnotation	Extension of Annotation for Mitab with a sourceLocator

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

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

Modifier and Type	Method	Description
void	AbstractMitabColumnFeeder.writeAnnotation(Annotation annotation)	Writes an annotation
void	MitabColumnFeeder.writeAnnotation(Annotation annotation)	Writes an annotation

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

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

Modifier and Type	Method	Description
static boolean	MitabUtils.isAnnotationAnInteractionTag(Annotation annot)	To know if a publication annotation is an interactionTag

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

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

Modifier and Type	Method	Description
static Annotation	InteractionUtils.collectComplexExpansionMethodFromAnnotations(Collection<? extends Annotation> annotations)	collectComplexExpansionMethodFromAnnotations
static Annotation	AnnotationUtils.collectFirstAnnotationWithTopic(Collection<? extends Annotation> annotations, String topicId, String topicName)	This method will return the first Annotation having this topicId/topic name It will return null if there are no Annotations with this topic id/name
static Annotation	AnnotationUtils.collectFirstAnnotationWithTopicAndValue(Collection<? extends Annotation> annotations, String topicId, String topicName, String value)	This method will return the first Annotation having this topicId/topic name It will return null if there are no Annotations with this topic id/name
static Annotation	AnnotationUtils.createAnnotation(String topicName, String name)	createAnnotation
static Annotation	AnnotationUtils.createAnnotation(String topicName, String topicMi, String name)	createAnnotation
static Annotation	AnnotationUtils.createCaution(String caution)	createCaution
static Annotation	AnnotationUtils.createComment(String comment)	createComment

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

Modifier and Type	Method	Description
static Collection<Annotation>	AnnotationUtils.collectAllAnnotationsHavingTopic(Collection<? extends Annotation> annots, String topicId, String topicName)	Collect all annotations having a specific topic
static Collection<Annotation>	AnnotationUtils.collectAllAnnotationsHavingTopic(Collection<? extends Annotation> annots, String topicId, String topicName, String value)	Collect all annotations having a specific topic and value

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

Modifier and Type	Method	Description
static boolean	AnnotationUtils.doesAnnotationHaveTopic(Annotation annotation, String topicId, String topicName)	To know if the annotation does have a specific topic
static boolean	AnnotationUtils.doesAnnotationHaveTopicAndValue(Annotation annotation, String topicId, String topicName, String value)	To know if the annotation does have a specific topic
static boolean	AnnotationUtils.doesAnnotationHaveTopicAndValueLike(Annotation annotation, String topicId, String topicName, String value)	To know if the annotation does have a specific topic and like value
static boolean	FeatureUtils.isFeatureRole(Annotation annotation)	isFeatureRole

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

Modifier and Type	Method	Description
static Collection<Annotation>	AnnotationUtils.collectAllAnnotationsHavingTopic(Collection<? extends Annotation> annots, String topicId, String topicName)	Collect all annotations having a specific topic
static Collection<Annotation>	AnnotationUtils.collectAllAnnotationsHavingTopic(Collection<? extends Annotation> annots, String topicId, String topicName, String value)	Collect all annotations having a specific topic and value
static Annotation	InteractionUtils.collectComplexExpansionMethodFromAnnotations(Collection<? extends Annotation> annotations)	collectComplexExpansionMethodFromAnnotations
static Annotation	AnnotationUtils.collectFirstAnnotationWithTopic(Collection<? extends Annotation> annotations, String topicId, String topicName)	This method will return the first Annotation having this topicId/topic name It will return null if there are no Annotations with this topic id/name
static Annotation	AnnotationUtils.collectFirstAnnotationWithTopicAndValue(Collection<? extends Annotation> annotations, String topicId, String topicName, String value)	This method will return the first Annotation having this topicId/topic name It will return null if there are no Annotations with this topic id/name
static void	AnnotationUtils.removeAllAnnotationsWithTopic(Collection<? extends Annotation> annotations, String topicId, String topicName)	Remove all annotations having this topic name/database id from the collection of annotations
static void	AnnotationUtils.removeAllAnnotationsWithTopicAndValue(Collection<? extends Annotation> annotations, String topicId, String topicName, String value)	Remove all annotations having this topic name/database id from the collection of annotations
static void	AnnotationUtils.removeAllAnnotationsWithTopicAndValueLike(Collection<? extends Annotation> annotations, String topicId, String topicName, String value)	Remove all annotations having this topic name/database id and like value from the collection of annotations

Uses of Annotation in psidev.psi.mi.jami.utils.comparator.annotation

Methods in psidev.psi.mi.jami.utils.comparator.annotation with parameters of type Annotation

Modifier and Type	Method	Description
static boolean	DefaultAnnotationComparator.areEquals(Annotation annotation1, Annotation annotation2)	Use DefaultAnnotationComparator to know if two annotations are equals.
static boolean	UnambiguousAnnotationComparator.areEquals(Annotation annotation1, Annotation annotation2)	Use UnambiguousAnnotationComparator to know if two annotations are equals.
int	AnnotationComparator.compare(Annotation annotation1, Annotation annotation2)	It compares first the topics and then the value (case insensitive) - Two annotations which are null are equals - The annotation which is not null is before null.
int	UnambiguousAnnotationComparator.compare(Annotation annotation1, Annotation annotation2)	It compares first the topics and then the value (case insensitive) - Two annotations which are null are equals - The annotation which is not null is before null.
static int	UnambiguousAnnotationComparator.hashCode(Annotation annot)	hashCode

Uses of Annotation in psidev.psi.mi.jami.xml.io.writer

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

Modifier and Type	Method	Description
void	AbstractXmlWriter.setAnnotationsWriter(PsiXmlElementWriter<Annotation> annotationsWriter)	Setter for the field annotationsWriter.
void	AbstractXmlWriter.setEntryAnnotations(Collection<Annotation> entryAnnotations)	Setter for the field entryAnnotations.

Uses of Annotation 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 Annotation

Modifier and Type	Method	Description
static PsiXmlElementWriter<Annotation>	PsiXmlElementWriterFactory.createAnnotationWriter(XMLStreamWriter streamWriter)	createAnnotationWriter.

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

Modifier and Type	Method	Description
static PsiXmlElementWriter<Allostery>	PsiXmlElementWriterFactory.createAllosteryWriter(XMLStreamWriter streamWriter, boolean expanded, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlPublicationWriter publicationWriter)	createAllosteryWriter.
static PsiXmlElementWriter<Preassembly>	PsiXmlElementWriterFactory.createPreassemblyWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlPublicationWriter publicationWriter)	createPreassemblyWriter.
static PsiXmlPublicationWriter	PsiXmlElementWriterFactory.createPublicationWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVersion version)	createPublicationWriter.
static PsiXmlXrefWriter	PsiXmlElementWriterFactory.createXrefWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Annotation> annotationWriter)	createXrefWriter.
void	PsiXmlPublicationWriter.writeAllPublicationAttributes(Publication object, Collection<Annotation> attributesToFilter)	writeAllPublicationAttributes.

Uses of Annotation 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 Annotation

Modifier and Type	Method	Description
PsiXmlElementWriter<Annotation>	AbstractXmlSourceWriter.getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Annotation>	XmlInteractorWriter.getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Annotation>	XmlOpenCvTermWriter.getAttributeWriter()	Getter for the field attributeWriter.

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

Modifier and Type	Method	Description
void	XmlAnnotationWriter.write(Annotation object)	write.

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

Modifier and Type	Method	Description
void	AbstractXmlSourceWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	XmlInteractorWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	XmlOpenCvTermWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.

Uses of Annotation 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 Annotation

Modifier and Type	Method	Description
PsiXmlElementWriter<Annotation>	AbstractXmlExperimentWriter.getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Annotation>	AbstractXmlFeatureWriter.getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Annotation>	AbstractXmlInteractionWriter.getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Annotation>	AbstractXmlParticipantWriter.getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Annotation>	AbstractXmlPublicationWriter.getAttributeWriter()	Getter for the field attributeWriter.

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

Modifier and Type	Method	Description
void	AbstractXmlExperimentWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	AbstractXmlFeatureWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	AbstractXmlInteractionWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	AbstractXmlParticipantWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	AbstractXmlPublicationWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	AbstractXmlPublicationWriter.writeAllPublicationAttributes(Publication object, Collection<Annotation> attributesToFilter)	writeAllPublicationAttributes.

Uses of Annotation 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 Annotation

Modifier and Type	Method	Description
PsiXmlElementWriter<Annotation>	AbstractXmlCooperativeEffectWriter.getAttributeWriter()	Getter for the field attributeWriter.

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

Modifier and Type	Method	Description
void	AbstractXmlCooperativeEffectWriter.setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.

Uses of Annotation 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 Annotation

Modifier and Type	Method	Description
PsiXmlElementWriter<Annotation>	XmlDbXrefWriter.getAnnotationWriter()	Getter for the field annotationWriter.

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

Modifier and Type	Method	Description
void	XmlDbXrefWriter.setAnnotationWriter(PsiXmlElementWriter<Annotation> annotationWriter)	Setter for the field annotationWriter.

Uses of Annotation in psidev.psi.mi.jami.xml.model

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

Modifier and Type	Method	Description
List<Annotation>	Entry.getAnnotations()	Getter for the field annotations.
List<Annotation>	AbstractBaseEntry.AbstractJAXBAnnotationsWrapper.getJAXBAttributes()

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

Modifier and Type	Method	Description
protected void	Entry.initialiseAnnotationsWith(List<Annotation> annotations)	initialiseAnnotationsWith.

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

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractBaseXmlInteractor.getAnnotations()	getAnnotations.
List<Annotation>	ExtendedPsiXmlXref.getAnnotations()	getAnnotations.
List<Annotation>	AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper.getJAXBAttributes()

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

Modifier and Type	Method	Description
protected void	AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper.initialiseAnnotationsWith(List<Annotation> annotations)

Uses of Annotation 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 Annotation

Modifier and Type	Method	Description
Collection<Annotation>	XmlBinaryInteractionEvidenceWrapper.getAnnotations()	The Collection of annotations describing the interaction.
Collection<Annotation>	XmlBinaryInteractionWrapper.getAnnotations()	The Collection of annotations describing the interaction.
Collection<Annotation>	XmlModelledBinaryInteractionWrapper.getAnnotations()	The Collection of annotations describing the interaction.

Uses of Annotation 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 Annotation

Modifier and Type	Method	Description
Collection<Annotation>	XmlModelledBinaryInteraction.getAnnotations()	Getter for the field annotations.
Collection<Annotation>	XmlModelledBinaryInteractionWrapper.getAnnotations()	The Collection of annotations describing the interaction.

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

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

Modifier and Type	Class	Description
class	AbstractXmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing
class	DefaultXmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing
class	XmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractXmlComplex.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlCvTerm.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlExperiment.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlFeature.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlInteraction.getAnnotations()	getAnnotations.
protected List<Annotation>	AbstractXmlInteraction.JAXBAttributeWrapper.getAnnotations()
Collection<Annotation>	AbstractXmlParticipant.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlParticipantPool.getAnnotations()	Collection of annotations describing the participant.
Collection<Annotation>	BibRef.getAnnotations()	getAnnotations.
Collection<Annotation>	XmlBasicInteractionComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlFeatureEvidenceWrapper.getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
Collection<Annotation>	XmlFeatureWrapper.getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
Collection<Annotation>	XmlInteractionEvidenceComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlModelledInteractionComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlParticipantEvidenceWrapper.getAnnotations()	Collection of annotations describing the participant.
Collection<Annotation>	XmlParticipantWrapper.getAnnotations()	Collection of annotations describing the participant.
List<Annotation>	XmlXref.getAnnotations()	getAnnotations.
List<Annotation>	AbstractXmlCvTerm.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlExperiment.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlFeature.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlInteraction.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlInteractor.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlParticipant.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlSource.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	BibRef.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	XmlXref.JAXBAttributeWrapper.getJAXBAttributes()

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

Modifier and Type	Method	Description
void	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.add(int index, Annotation element)
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.add(Annotation annotation)
protected boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.processAnnotation(Integer index, Annotation annotation)

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

Modifier and Type	Method	Description
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.addAll(int index, Collection<? extends Annotation> c)
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.addAll(Collection<? extends Annotation> c)
protected void	AbstractXmlCvTerm.JAXBAttributeWrapper.initialiseAnnotationsWith(List<Annotation> annotations)
protected void	AbstractXmlInteraction.JAXBAttributeWrapper.initialiseAnnotationsWith(List<Annotation> annots)

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

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

Modifier and Type	Class	Description
class	AbstractXmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing
class	DefaultXmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing
class	XmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractXmlComplex.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlCvTerm.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlExperiment.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlFeature.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlInteraction.getAnnotations()	getAnnotations.
protected List<Annotation>	AbstractXmlInteraction.JAXBAttributeWrapper.getAnnotations()
Collection<Annotation>	AbstractXmlParticipant.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlParticipantPool.getAnnotations()	Collection of annotations describing the participant.
Collection<Annotation>	BibRef.getAnnotations()	getAnnotations.
Collection<Annotation>	XmlBasicInteractionComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlFeatureEvidenceWrapper.getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
Collection<Annotation>	XmlFeatureWrapper.getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
Collection<Annotation>	XmlInteractionEvidenceComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlModelledInteractionComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlParticipantEvidenceWrapper.getAnnotations()	Collection of annotations describing the participant.
Collection<Annotation>	XmlParticipantWrapper.getAnnotations()	Collection of annotations describing the participant.
List<Annotation>	XmlXref.getAnnotations()	getAnnotations.
List<Annotation>	AbstractXmlCvTerm.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlExperiment.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlFeature.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlInteraction.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlInteractor.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlParticipant.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlSource.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	BibRef.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	XmlXref.JAXBAttributeWrapper.getJAXBAttributes()

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

Modifier and Type	Method	Description
void	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.add(int index, Annotation element)
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.add(Annotation annotation)
protected boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.processAnnotation(Integer index, Annotation annotation)

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

Modifier and Type	Method	Description
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.addAll(int index, Collection<? extends Annotation> c)
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.addAll(Collection<? extends Annotation> c)
protected void	AbstractXmlCvTerm.JAXBAttributeWrapper.initialiseAnnotationsWith(List<Annotation> annotations)
protected void	AbstractXmlInteraction.JAXBAttributeWrapper.initialiseAnnotationsWith(List<Annotation> annots)

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

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

Modifier and Type	Class	Description
class	AbstractXmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing
class	DefaultXmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing
class	XmlAnnotation	Xml implementation of an Annotation The JAXB binding is designed to be read-only and is not designed for writing

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractXmlComplex.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlCooperativeEffect.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlCvTerm.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlExperiment.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlFeature.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlInteraction.getAnnotations()	getAnnotations.
protected List<Annotation>	AbstractXmlInteraction.JAXBAttributeWrapper.getAnnotations()
Collection<Annotation>	AbstractXmlParticipant.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractXmlParticipantPool.getAnnotations()	Collection of annotations describing the participant.
Collection<Annotation>	BibRef.getAnnotations()	getAnnotations.
Collection<Annotation>	XmlBasicInteractionComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlFeatureEvidenceWrapper.getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
Collection<Annotation>	XmlFeatureWrapper.getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
Collection<Annotation>	XmlInteractionEvidenceComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlModelledInteraction.getAnnotations()	getAnnotations.
Collection<Annotation>	XmlModelledInteractionComplexWrapper.getAnnotations()	Collection of annotations for an interactor.
Collection<Annotation>	XmlParticipantEvidenceWrapper.getAnnotations()	Collection of annotations describing the participant.
Collection<Annotation>	XmlParticipantWrapper.getAnnotations()	Collection of annotations describing the participant.
List<Annotation>	XmlXref.getAnnotations()	getAnnotations.
List<Annotation>	AbstractXmlCooperativeEffect.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlCvTerm.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlExperiment.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlFeature.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlInteraction.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlInteractor.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlParticipant.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	AbstractXmlSource.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	BibRef.JAXBAttributeWrapper.getJAXBAttributes()
List<Annotation>	XmlXref.JAXBAttributeWrapper.getJAXBAttributes()

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

Modifier and Type	Method	Description
void	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.add(int index, Annotation element)
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.add(Annotation annotation)
protected boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.processAnnotation(Integer index, Annotation annotation)

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

Modifier and Type	Method	Description
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.addAll(int index, Collection<? extends Annotation> c)
boolean	AbstractXmlInteraction.JAXBAttributeWrapper.JAXBAttributeList.addAll(Collection<? extends Annotation> c)
protected void	AbstractXmlCvTerm.JAXBAttributeWrapper.initialiseAnnotationsWith(List<Annotation> annotations)
protected void	AbstractXmlInteraction.JAXBAttributeWrapper.initialiseAnnotationsWith(List<Annotation> annots)

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

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractFeatureRef.getAnnotations()	getAnnotations.

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

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractComplexRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractExperimentRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractInteractorRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractParticipantRef.getAnnotations()	getAnnotations.

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

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractComplexRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractExperimentRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractInteractorRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractParticipantRef.getAnnotations()	getAnnotations.

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

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

Modifier and Type	Method	Description
Collection<Annotation>	AbstractComplexRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractExperimentRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractInteractorRef.getAnnotations()	getAnnotations.
Collection<Annotation>	AbstractParticipantRef.getAnnotations()	getAnnotations.

Uses of Annotation in psidev.psi.mi.jami.xml.model.xml253

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

Modifier and Type	Method	Description
List<Annotation>	AbstractEntry.JAXBAnnotationsWrapper.getJAXBAttributes()

Uses of Annotation in psidev.psi.mi.jami.xml.model.xml254

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

Modifier and Type	Method	Description
List<Annotation>	AbstractEntry.JAXBAnnotationsWrapper.getJAXBAttributes()

Uses of Annotation in psidev.psi.mi.jami.xml.model.xml30

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

Modifier and Type	Method	Description
List<Annotation>	AbstractEntry.JAXBAnnotationsWrapper.getJAXBAttributes()

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

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

Modifier and Type	Method	Description
static CooperativeEffect	PsiXmlUtils.extractCooperativeEffectFrom(PsiXmlVersion version, Collection<Annotation> annots, Collection<Experiment> experiments, PsiXmlParserListener listener)	extractCooperativeEffectFrom.