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

Packages that use Experiment

Package	Description
psidev.psi.mi.jami.binary.impl
psidev.psi.mi.jami.commons
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.datasource
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.log
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.imex
psidev.psi.mi.jami.imex.actions
psidev.psi.mi.jami.imex.actions.impl
psidev.psi.mi.jami.imex.listener
psidev.psi.mi.jami.imex.listener.impl
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.utils
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator.experiment
psidev.psi.mi.jami.xml
psidev.psi.mi.jami.xml.cache
psidev.psi.mi.jami.xml.io.writer.compact
psidev.psi.mi.jami.xml.io.writer.elements
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30
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.listener
psidev.psi.mi.jami.xml.model.extension
psidev.psi.mi.jami.xml.model.extension.binary
psidev.psi.mi.jami.xml.model.extension.datasource
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300
psidev.psi.mi.jami.xml.model.reference.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300
psidev.psi.mi.jami.xml.model.xml253
psidev.psi.mi.jami.xml.model.xml254
psidev.psi.mi.jami.xml.model.xml30

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

Methods in psidev.psi.mi.jami.binary.impl that return Experiment

Modifier and Type	Method	Description
Experiment	BinaryInteractionEvidenceWrapper.getExperiment()	getExperiment
Experiment	DefaultBinaryInteractionEvidence.getExperiment()	Getter for the field experiment.

Methods in psidev.psi.mi.jami.binary.impl with parameters of type Experiment

Modifier and Type	Method	Description
void	BinaryInteractionEvidenceWrapper.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	DefaultBinaryInteractionEvidence.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	BinaryInteractionEvidenceWrapper.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	DefaultBinaryInteractionEvidence.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction

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

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

Modifier and Type	Method	Description
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, boolean writeComplexAsInteractors, boolean extended, 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.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 Experiment in psidev.psi.mi.jami.crosslink.extension

Constructors in psidev.psi.mi.jami.crosslink.extension with parameters of type Experiment

Constructor	Description
CsvInteractionEvidence(Experiment experiment)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, CvTerm type)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for CsvInteractionEvidence.

Uses of Experiment in psidev.psi.mi.jami.datasource

Methods in psidev.psi.mi.jami.datasource that return types with arguments of type Experiment

Modifier and Type	Method	Description
Iterator<Experiment>	ExperimentStream.getExperimentsIterator()	The experiments iterator for this datasource.

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

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

Modifier and Type	Method	Description
protected void	FullExperimentEnricher.mergerVariableParameters(Experiment experimentToEnrich, Experiment objectSource, boolean remove)	mergerVariableParameters.
protected void	FullExperimentEnricher.processAnnotations(Experiment experimentToEnrich, Experiment objectSource)	processAnnotations.
protected void	FullExperimentUpdater.processAnnotations(Experiment experimentToEnrich, Experiment objectSource)	processAnnotations.
protected void	FullExperimentEnricher.processConfidences(Experiment experimentToEnrich, Experiment objectSource)	processConfidences.
protected void	FullExperimentUpdater.processConfidences(Experiment experimentToEnrich, Experiment objectSource)	processConfidences.
void	FullExperimentUpdater.processExperiment(Experiment experimentToEnrich, Experiment objectSource)	processExperiment.
protected void	FullExperimentEnricher.processOtherProperties(Experiment experimentToEnrich)	processOtherProperties.
protected void	FullExperimentEnricher.processOtherProperties(Experiment experimentToEnrich, Experiment objectSource)	processOtherProperties.
protected void	FullExperimentEnricher.processVariableParameters(Experiment experimentToEnrich, Experiment objectSource)	processVariableParameters.
protected void	FullExperimentUpdater.processVariableParameters(Experiment experimentToEnrich, Experiment objectSource)	processVariableParameters.
protected void	FullExperimentEnricher.processXrefs(Experiment experimentToEnrich, Experiment objectSource)	processXrefs.
protected void	FullExperimentUpdater.processXrefs(Experiment experimentToEnrich, Experiment objectSource)	processXrefs.

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

Methods in psidev.psi.mi.jami.enricher.impl.minimal that return Experiment

Modifier and Type	Method	Description
Experiment	MinimalExperimentEnricher.find(Experiment objectToEnrich)	find.

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

Modifier and Type	Method	Description
void	MinimalExperimentEnricher.enrich(Experiment experimentToEnrich, Experiment objectSource)	enrich.
Experiment	MinimalExperimentEnricher.find(Experiment objectToEnrich)	find.
protected void	MinimalExperimentEnricher.onEnrichedVersionNotFound(Experiment experimentToEnrich)	onEnrichedVersionNotFound.
void	MinimalExperimentEnricher.processExperiment(Experiment experimentToEnrich)	processExperiment.
void	MinimalExperimentEnricher.processExperiment(Experiment experimentToEnrich, Experiment objectSource)	processExperiment.
protected void	MinimalExperimentEnricher.processInteractionDetectionMethod(Experiment experimentToEnrich)	processInteractionDetectionMethod.
protected void	MinimalExperimentEnricher.processInteractionDetectionMethod(Experiment experimentToEnrich, Experiment objectSource)	processInteractionDetectionMethod.
protected void	MinimalExperimentUpdater.processInteractionDetectionMethod(Experiment experimentToEnrich, Experiment objectSource)	processInteractionDetectionMethod.
protected void	MinimalExperimentEnricher.processOrganism(Experiment experimentToEnrich)	processOrganism.
protected void	MinimalExperimentEnricher.processOrganism(Experiment experimentToEnrich, Experiment objectSource)	processOrganism.
protected void	MinimalExperimentUpdater.processOrganism(Experiment experimentToEnrich, Experiment objectSource)	processOrganism.
protected void	MinimalExperimentEnricher.processOtherProperties(Experiment experimentToEnrich)	processOtherProperties.
protected void	MinimalExperimentEnricher.processOtherProperties(Experiment experimentToEnrich, Experiment objectSource)	processOtherProperties.
protected void	MinimalExperimentEnricher.processPublication(Experiment experimentToEnrich)	processPublication.
protected void	MinimalExperimentEnricher.processPublication(Experiment experimentToEnrich, Experiment objectSource)	processPublication.
protected void	MinimalExperimentUpdater.processPublication(Experiment experimentToEnrich, Experiment objectSource)	processPublication.

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

Modifier and Type	Method	Description
void	MinimalExperimentEnricher.enrich(Collection<Experiment> objects)	enrich.

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

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

Modifier and Type	Method	Description
void	ExperimentEnricherListenerManager.onAddedAnnotation(Experiment experiment, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ExperimentEnricherListenerManager.onAddedConfidence(Experiment experiment, Confidence added)	Listen to the event where a confidence has been added to the object confidences.
void	ExperimentEnricherListenerManager.onAddedVariableParameter(Experiment experiment, VariableParameter added)	Listen to the event where a parameter has been added to the object parameters.
void	ExperimentEnricherListenerManager.onAddedXref(Experiment experiment, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractionEvidenceEnricherListenerManager.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	ExperimentEnricherListenerManager.onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)	onHostOrganismUpdate
void	ExperimentEnricherListenerManager.onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)	onInteractionDetectionMethodUpdate
void	ExperimentEnricherListenerManager.onPublicationUpdate(Experiment experiment, Publication oldPublication)	onPublicationUpdate
void	ExperimentEnricherListenerManager.onRemovedAnnotation(Experiment experiment, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ExperimentEnricherListenerManager.onRemovedConfidence(Experiment experiment, Confidence removed)	Listen to the event where a confidence has been removed from the object confidences.
void	ExperimentEnricherListenerManager.onRemovedVariableParameter(Experiment o, VariableParameter removed)	Listen to the event where a parameter has been removed from the object parameters.
void	ExperimentEnricherListenerManager.onRemovedXref(Experiment experiment, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.

Uses of Experiment in psidev.psi.mi.jami.enricher.listener.impl.log

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

Modifier and Type	Method	Description
void	ExperimentEnricherLogger.onEnrichmentComplete(Experiment experiment, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	ExperimentEnricherLogger.onEnrichmentError(Experiment object, String message, Exception e)	onEnrichmentError.

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

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

Modifier and Type	Method	Description
void	ExperimentEnricherStatisticsWriter.onAddedAnnotation(Experiment o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ExperimentEnricherStatisticsWriter.onAddedConfidence(Experiment o, Confidence added)	Listen to the event where a confidence has been added to the object confidences.
void	ExperimentEnricherStatisticsWriter.onAddedVariableParameter(Experiment o, VariableParameter added)	Listen to the event where a parameter has been added to the object parameters.
void	ExperimentEnricherStatisticsWriter.onAddedXref(Experiment o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractionEvidenceEnricherStatisticsWriter.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	ExperimentEnricherStatisticsWriter.onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)	onHostOrganismUpdate
void	ExperimentEnricherStatisticsWriter.onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)	onInteractionDetectionMethodUpdate
void	ExperimentEnricherStatisticsWriter.onPublicationUpdate(Experiment experiment, Publication oldPublication)	onPublicationUpdate
void	ExperimentEnricherStatisticsWriter.onRemovedAnnotation(Experiment o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ExperimentEnricherStatisticsWriter.onRemovedConfidence(Experiment o, Confidence removed)	Listen to the event where a confidence has been removed from the object confidences.
void	ExperimentEnricherStatisticsWriter.onRemovedVariableParameter(Experiment o, VariableParameter removed)	Listen to the event where a parameter has been removed from the object parameters.
void	ExperimentEnricherStatisticsWriter.onRemovedXref(Experiment o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.

Uses of Experiment in psidev.psi.mi.jami.imex

Methods in psidev.psi.mi.jami.imex with parameters of type Experiment

Modifier and Type	Method	Description
protected void	ImexExperimentUpdater.processAnnotations(Experiment experimentToEnrich, Experiment objectSource)	processAnnotations.
protected void	ImexExperimentUpdater.processConfidences(Experiment experimentToEnrich, Experiment objectSource)	processConfidences.
protected void	ImexExperimentUpdater.processInteractionDetectionMethod(Experiment experimentToEnrich)	processInteractionDetectionMethod.
protected void	ImexExperimentUpdater.processInteractionDetectionMethod(Experiment experimentToEnrich, Experiment objectSource)	processInteractionDetectionMethod.
protected void	ImexExperimentUpdater.processOrganism(Experiment experimentToEnrich)	processOrganism.
protected void	ImexExperimentUpdater.processOrganism(Experiment experimentToEnrich, Experiment objectSource)	processOrganism.
protected void	ImexExperimentUpdater.processOtherProperties(Experiment experimentToEnrich)	processOtherProperties.
protected void	ImexExperimentUpdater.processVariableParameters(Experiment experimentToEnrich, Experiment objectSource)	processVariableParameters.
protected void	ImexExperimentUpdater.processXrefs(Experiment experimentToEnrich, Experiment objectSource)	processXrefs.

Uses of Experiment in psidev.psi.mi.jami.imex.actions

Methods in psidev.psi.mi.jami.imex.actions with parameters of type Experiment

Modifier and Type	Method	Description
boolean	ImexAssigner.updateImexIdentifierForExperiment(Experiment experiment, String imexId)	Add a IMEx primary reference to the experiment

Uses of Experiment in psidev.psi.mi.jami.imex.actions.impl

Methods in psidev.psi.mi.jami.imex.actions.impl with parameters of type Experiment

Modifier and Type	Method	Description
boolean	ImexAssignerImpl.updateImexIdentifierForExperiment(Experiment experiment, String imexId)	Add a IMEx primary reference to the experiment

Uses of Experiment in psidev.psi.mi.jami.imex.listener

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

Modifier and Type	Method	Description
void	ExperimentImexEnricherListener.onImexIdAssigned(Experiment experiment, String imex)	onImexIdAssigned.
void	ExperimentImexEnricherListener.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.

Uses of Experiment in psidev.psi.mi.jami.imex.listener.impl

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

Modifier and Type	Method	Description
void	ExperimentImexEnricherListenerManager.onImexIdAssigned(Experiment experiment, String imex)	onImexIdAssigned.
void	ExperimentImexEnricherLogger.onImexIdAssigned(Experiment experiment, String imex)	onImexIdAssigned.
void	ExperimentImexEnricherStatisticsWriter.onImexIdAssigned(Experiment experiment, String imex)	onImexIdAssigned.
void	ExperimentImexEnricherListenerManager.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	ExperimentImexEnricherLogger.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	ExperimentImexEnricherStatisticsWriter.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.

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

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

Modifier and Type	Method	Description
void	ExperimentChangeListener.onAddedVariableParameter(Experiment o, VariableParameter added)	Listen to the event where a parameter has been added to the object parameters.
void	InteractionEvidenceChangeListener.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	ExperimentChangeListener.onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)	onHostOrganismUpdate
void	ExperimentChangeListener.onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)	onInteractionDetectionMethodUpdate
void	ExperimentChangeListener.onPublicationUpdate(Experiment experiment, Publication oldPublication)	onPublicationUpdate
void	ExperimentChangeListener.onRemovedVariableParameter(Experiment o, VariableParameter removed)	Listen to the event where a parameter has been removed from the object parameters.

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

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

Modifier and Type	Method	Description
void	ExperimentChangeLogger.onAddedAnnotation(Experiment experiment, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	ExperimentChangeLogger.onAddedConfidence(Experiment experiment, Confidence added)	Listen to the event where a confidence has been added to the object confidences.
void	ExperimentChangeLogger.onAddedVariableParameter(Experiment experiment, VariableParameter addedParameter)	Listen to the event where a parameter has been added to the object parameters.
void	ExperimentChangeLogger.onAddedXref(Experiment experiment, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractionEvidenceChangeLogger.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	ExperimentChangeLogger.onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)	onHostOrganismUpdate
void	ExperimentChangeLogger.onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)	onInteractionDetectionMethodUpdate
void	ExperimentChangeLogger.onPublicationUpdate(Experiment experiment, Publication oldPublication)	onPublicationUpdate
void	ExperimentChangeLogger.onRemovedAnnotation(Experiment experiment, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	ExperimentChangeLogger.onRemovedConfidence(Experiment experiment, Confidence removed)	Listen to the event where a confidence has been removed from the object confidences.
void	ExperimentChangeLogger.onRemovedVariableParameter(Experiment experiment, VariableParameter removedParameter)	Listen to the event where a parameter has been removed from the object parameters.
void	ExperimentChangeLogger.onRemovedXref(Experiment experiment, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.

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

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

Modifier and Type	Interface	Description
interface	NamedExperiment	A named experiment is an experiment with a shortname, fullname and aliases

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

Modifier and Type	Method	Description
<E extends Experiment> Collection<E>	Publication.getExperiments()	The curated experiments which have been described in the publication.

Methods in psidev.psi.mi.jami.model that return Experiment

Modifier and Type	Method	Description
Experiment	InteractionEvidence.getExperiment()	The experiment which determined the interaction.
Experiment	VariableParameter.getExperiment()	The experiment where this variableParameter has been used.

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

Modifier and Type	Method	Description
boolean	Publication.addExperiment(Experiment exp)	This method will add the experiment and set the publication of the new experiment to this current publication
boolean	Publication.removeExperiment(Experiment exp)	This method will remove the experiment and set the publication of the removed experiment to null.
void	InteractionEvidence.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	VariableParameter.setExperiment(Experiment experiment)	Sets the experiment for this variableParameter
void	InteractionEvidence.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	VariableParameter.setExperimentAndAddVariableParameter(Experiment experiment)	Sets the experiment for this variableParameter and add this variableParameter to the list of variableParameters of this experiment.

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

Modifier and Type	Method	Description
boolean	Publication.addAllExperiments(Collection<? extends Experiment> exp)	This method will add all the experiments and set the publication of the new experiments to this current publication
boolean	Publication.removeAllExperiments(Collection<? extends Experiment> exp)	This method will remove the experiments and set the publication of the removed experiments to null.

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

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

Modifier and Type	Class	Description
class	DefaultExperiment	Default implementation for Experiment Notes: The equals and hashcode methods have NOT been overridden because the Experiment object is a complex object.
class	DefaultNamedExperiment	Default implementation for NamedExperiment.

Methods in psidev.psi.mi.jami.model.impl that return Experiment

Modifier and Type	Method	Description
Experiment	DefaultInteractionEvidence.getExperiment()	Getter for the field experiment.
Experiment	DefaultVariableParameter.getExperiment()	Getter for the field experiment.

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

Modifier and Type	Method	Description
Collection<Experiment>	DefaultPublication.getExperiments()	Getter for the field experiments.

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

Modifier and Type	Method	Description
boolean	DefaultPublication.addExperiment(Experiment exp)	This method will add the experiment and set the publication of the new experiment to this current publication
boolean	DefaultPublication.removeExperiment(Experiment exp)	This method will remove the experiment and set the publication of the removed experiment to null.
void	DefaultInteractionEvidence.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	DefaultVariableParameter.setExperiment(Experiment experiment)	Sets the experiment for this variableParameter
void	DefaultInteractionEvidence.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	DefaultVariableParameter.setExperimentAndAddVariableParameter(Experiment experiment)	Sets the experiment for this variableParameter and add this variableParameter to the list of variableParameters of this experiment.

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

Modifier and Type	Method	Description
boolean	DefaultPublication.addAllExperiments(Collection<? extends Experiment> exps)	This method will add all the experiments and set the publication of the new experiments to this current publication
protected void	DefaultPublication.initialiseExperimentsWith(Collection<Experiment> experiments)	initialiseExperimentsWith
boolean	DefaultPublication.removeAllExperiments(Collection<? extends Experiment> exps)	This method will remove the experiments and set the publication of the removed experiments to null.

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

Constructor	Description
DefaultInteractionEvidence(Experiment experiment)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, CvTerm type)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, CvTerm type)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultVariableParameter(String description, Experiment experiment)	Constructor for DefaultVariableParameter.
DefaultVariableParameter(String description, Experiment experiment, CvTerm unit)	Constructor for DefaultVariableParameter.

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

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

Modifier and Type	Class	Description
class	MitabExperiment	Mitab extension for Experiment.

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

Constructor	Description
MitabInteractionEvidence(Experiment experiment)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, CvTerm type)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for MitabInteractionEvidence.

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

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

Modifier and Type	Method	Description
static Experiment	ExperimentUtils.createBasicExperimentForComplexes()	createBasicExperimentForComplexes
static Experiment	ExperimentUtils.createBasicExperimentForComplexes(int taxid)	createBasicExperimentForComplexes
static Experiment	ExperimentUtils.createBasicExperimentForComplexes(int taxid, String name)	createBasicExperimentForComplexes
static Experiment	ExperimentUtils.createBasicExperimentForModelledInteractions()	createBasicExperimentForModelledInteractions
static Experiment	ExperimentUtils.createExperiment(String pubmedId, CvTerm interactionDetectionMethod, Organism hostOrganism)	createExperiment
static Experiment	ExperimentUtils.createExperimentWithoutPublication()	createExperimentWithoutPublication
static Experiment	ExperimentUtils.createUnknownBasicExperiment()	createUnknownBasicExperiment

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

Modifier and Type	Method	Description
static CvTerm	ExperimentUtils.extractMostCommonParticipantDetectionMethodFrom(Experiment exp)	Compare all participant identification methods in all participant evidences from all the interactions evidences.
static String	ExperimentUtils.getDoiId(Experiment exp)	getDoiId
static Xref	ExperimentUtils.getDoiReference(Experiment exp)	getDoiReference
static String	ExperimentUtils.getPubmedId(Experiment exp)	getPubmedId
static Xref	ExperimentUtils.getPubmedReference(Experiment exp)	getPubmedReference

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

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

Modifier and Type	Method	Description
static void	ExperimentCloner.copyAndOverrideExperimentProperties(Experiment source, Experiment target)	This method will copy properties of experiment source in experiment target and will override all the other properties of Target experiment.
static void	ExperimentCloner.copyAndOverrideExperimentPropertiesAndInteractionEvidences(Experiment source, Experiment target)	This method will copy properties of experiment source in experiment target and will override all the other properties of Target experiment.

Uses of Experiment in psidev.psi.mi.jami.utils.comparator.experiment

Methods in psidev.psi.mi.jami.utils.comparator.experiment with parameters of type Experiment

Modifier and Type	Method	Description
static boolean	DefaultCuratedExperimentComparator.areEquals(Experiment experiment1, Experiment experiment2)	Use DefaultCuratedExperimentComparator to know if two experiment are equals.
static boolean	DefaultExperimentComparator.areEquals(Experiment experiment1, Experiment experiment2)	Use DefaultExperimentComparator to know if two experiment are equals.
static boolean	UnambiguousCuratedExperimentComparator.areEquals(Experiment experiment1, Experiment experiment2)	Use UnambiguousExperimentComparator to know if two experiment are equals.
static boolean	UnambiguousExperimentComparator.areEquals(Experiment experiment1, Experiment experiment2)	Use UnambiguousExperimentComparator to know if two experiment are equals.
int	ExperimentComparator.compare(Experiment experiment1, Experiment experiment2)	It will look first at the publications using a AbstractPublicationComparator.
int	UnambiguousCuratedExperimentComparator.compare(Experiment experiment1, Experiment experiment2)
int	UnambiguousExperimentComparator.compare(Experiment experiment1, Experiment experiment2)
static int	UnambiguousCuratedExperimentComparator.hashCode(Experiment exp)	hashCode
static int	UnambiguousExperimentComparator.hashCode(Experiment exp)	hashCode

Uses of Experiment in psidev.psi.mi.jami.xml

Methods in psidev.psi.mi.jami.xml with parameters of type Experiment

Modifier and Type	Method	Description
void	XmlEntryContext.registerExperiment(int id, Experiment o)	registerExperiment.

Uses of Experiment in psidev.psi.mi.jami.xml.cache

Methods in psidev.psi.mi.jami.xml.cache that return Experiment

Modifier and Type	Method	Description
Experiment	InMemoryPsiXmlCache.getExperiment(int id)	getExperiment.
Experiment	PsiXmlFileIndexCache.getExperiment(int id)	getExperiment.
Experiment	PsiXmlIdCache.getExperiment(int id)	getExperiment.

Methods in psidev.psi.mi.jami.xml.cache with parameters of type Experiment

Modifier and Type	Method	Description
int	InMemoryIdentityObjectCache.extractIdForExperiment(Experiment o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
int	InMemoryLightIdentityObjectCache.extractIdForExperiment(Experiment o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
int	PsiXmlObjectCache.extractIdForExperiment(Experiment o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
void	InMemoryPsiXmlCache.registerExperiment(int id, Experiment object)	Register an experiment with an id
void	PsiXmlFileIndexCache.registerExperiment(int id, Experiment object)	Register an experiment with an id
void	PsiXmlIdCache.registerExperiment(int id, Experiment object)	Register an experiment with an id

Uses of Experiment in psidev.psi.mi.jami.xml.io.writer.compact

Methods in psidev.psi.mi.jami.xml.io.writer.compact that return types with arguments of type Experiment

Modifier and Type	Method	Description
protected Set<Experiment>	AbstractCompactXmlWriter.getExperiments()	Getter for the field experiments.

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

Modifier and Type	Method	Description
void	AbstractCompactXmlMixWriter.setExperimentSet(Set<Experiment> experiments)	setExperimentSet.
void	AbstractCompactXmlWriter.setExperimentSet(Set<Experiment> experiments)	setExperimentSet.

Uses of Experiment in psidev.psi.mi.jami.xml.io.writer.elements

Methods in psidev.psi.mi.jami.xml.io.writer.elements that return Experiment

Modifier and Type	Method	Description
Experiment	PsiXmlInteractionWriter.extractDefaultExperimentFrom(T interaction)	extractDefaultExperimentFrom.
Experiment	PsiXmlInteractionWriter.getDefaultExperiment()	The default experiment that will be used to write a valid XML file but is not a real experiment attached to the interaction.
Experiment	PsiXmlParameterWriter.getDefaultExperiment()	The default experiment that will be used to write a valid XML file but is not a real experiment attached to the interaction.

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

Modifier and Type	Method	Description
List<Experiment>	PsiXmlExtendedInteractionWriter.extractDefaultExperimentsFrom(T interaction)	extractDefaultExperimentsFrom.
List<Experiment>	PsiXmlExtendedInteractionWriter.getDefaultExperiments()	The default experiments that will be used to write a valid XML file but are not real experiments attached to the interaction.

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

Modifier and Type	Method	Description
CvTerm	PsiXmlExperimentWriter.extractDefaultParticipantIdentificationMethod(Experiment exp)	extractDefaultParticipantIdentificationMethod.
void	PsiXmlInteractionWriter.setDefaultExperiment(Experiment exp)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	PsiXmlParameterWriter.setDefaultExperiment(Experiment exp)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
CvTerm	PsiXmlExperimentWriter.writeExperiment(Experiment exp)	writeExperiment.

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

Modifier and Type	Method	Description
void	PsiXmlExtendedInteractionWriter.setDefaultExperiments(List<Experiment> exp)	Sets the default experiments that will be used to write a valid XML file even if the interaction does not have any valid experiment

Uses of Experiment 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 Experiment

Modifier and Type	Method	Description
Experiment	AbstractXmlInteractionEvidenceWriter.extractDefaultExperimentFrom(I interaction)	extractDefaultExperimentFrom.
Experiment	AbstractXmlInteractionWriter.extractDefaultExperimentFrom(T interaction)	extractDefaultExperimentFrom.
Experiment	AbstractXmlInteractionWriter.getDefaultExperiment()	Getter for the field defaultExperiment.
Experiment	AbstractXmlParameterWriter.getDefaultExperiment()	The default experiment that will be used to write a valid XML file but is not a real experiment attached to the interaction.

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

Modifier and Type	Method	Description
CvTerm	AbstractXmlExperimentWriter.extractDefaultParticipantIdentificationMethod(Experiment exp)	extractDefaultParticipantIdentificationMethod.
void	AbstractXmlInteractionEvidenceWriter.setDefaultExperiment(Experiment defaultExperiment)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	AbstractXmlInteractionWriter.setDefaultExperiment(Experiment defaultExperiment)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	AbstractXmlModelledInteractionWriter.setDefaultExperiment(Experiment defaultExperiment)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	AbstractXmlParameterWriter.setDefaultExperiment(Experiment exp)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	AbstractXmlExperimentWriter.write(Experiment object)	write.
protected void	AbstractXmlExperimentWriter.writeAttributes(Experiment object)	writeAttributes.
protected void	AbstractXmlExperimentWriter.writeConfidences(Experiment object)	writeConfidences.
CvTerm	AbstractXmlExperimentWriter.writeExperiment(Experiment object)	writeExperiment.
protected abstract void	AbstractXmlExperimentWriter.writeExperimentXrefs(Experiment object, String imexId)	writeExperimentXrefs.
protected void	AbstractXmlExperimentWriter.writeHostOrganism(Experiment object)	writeHostOrganism.
protected void	AbstractXmlExperimentWriter.writeInteractiondetectionMethod(Experiment object)	writeInteractiondetectionMethod.
protected void	AbstractXmlExperimentWriter.writeNames(Experiment object)	writeNames.
protected abstract void	AbstractXmlExperimentWriter.writeOtherAttributes(Experiment object, boolean needToWriteAttributeList)	writeOtherAttributes.
protected void	AbstractXmlExperimentWriter.writeOtherProperties(Experiment object)	writeOtherProperties.
protected CvTerm	AbstractXmlExperimentWriter.writeParticipantIdentificationMethod(Experiment object)	writeParticipantIdentificationMethod.
protected void	AbstractXmlExperimentWriter.writePublicationAndXrefs(Experiment object)	writePublicationAndXrefs.
protected abstract void	AbstractXmlExperimentWriter.writeVariableParameters(Experiment object)	writeVariableParameters.
protected void	AbstractXmlExperimentWriter.writeXrefFromExperimentXrefs(Experiment object, String imexId)	writeXrefFromExperimentXrefs.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25 that return Experiment

Modifier and Type	Method	Description
Experiment	AbstractXmlModelledInteractionWriter.extractDefaultExperimentFrom(I interaction)	extractDefaultExperimentFrom.

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

Modifier and Type	Method	Description
void	AbstractXmlModelledInteractionWriter.setDefaultExperiment(Experiment defaultExperiment)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment

Uses of Experiment 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 Experiment

Modifier and Type	Method	Description
Experiment	XmlComplexWriter.extractDefaultExperimentFrom(Complex interaction)	extractDefaultExperimentFrom.

Uses of Experiment 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 Experiment

Modifier and Type	Method	Description
Experiment	XmlComplexWriter.extractDefaultExperimentFrom(Complex interaction)	extractDefaultExperimentFrom.

Uses of Experiment 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 Experiment

Modifier and Type	Method	Description
List<Experiment>	AbstractXmlInteractionEvidenceWriter.extractDefaultExperimentsFrom(I interaction)	extractDefaultExperimentsFrom.
List<Experiment>	AbstractXmlInteractionEvidenceWriter.getDefaultExperiments()	The default experiments that will be used to write a valid XML file but are not real experiments attached to the interaction.
List<Experiment>	AbstractXmlModelledInteractionWriter.getDefaultExperiments()	The default experiments that will be used to write a valid XML file but are not real experiments attached to the interaction.

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

Modifier and Type	Method	Description
void	AbstractXmlInteractionEvidenceWriter.setDefaultExperiments(List<Experiment> exp)	Sets the default experiments that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	AbstractXmlModelledInteractionWriter.setDefaultExperiments(List<Experiment> exp)	Sets the default experiments that will be used to write a valid XML file even if the interaction does not have any valid experiment

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml25 that return Experiment

Modifier and Type	Method	Description
Experiment	XmlComplexWriter.extractDefaultExperimentFrom(Complex interaction)	extractDefaultExperimentFrom.

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

Modifier and Type	Method	Description
List<Experiment>	XmlComplexWriter.extractDefaultExperimentsFrom(Complex interaction)	extractDefaultExperimentsFrom.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml25 that return Experiment

Modifier and Type	Method	Description
Experiment	XmlComplexWriter.extractDefaultExperimentFrom(Complex interaction)	extractDefaultExperimentFrom.

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

Modifier and Type	Method	Description
List<Experiment>	XmlComplexWriter.extractDefaultExperimentsFrom(Complex interaction)	extractDefaultExperimentsFrom.

Uses of Experiment 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 Experiment

Modifier and Type	Method	Description
Experiment	AbstractXmlModelledInteractionWriter.extractDefaultExperimentFrom(I interaction)	extractDefaultExperimentFrom.

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

Modifier and Type	Method	Description
List<Experiment>	AbstractXmlInteractionWriter.extractDefaultExperimentsFrom(I interaction)	extractDefaultExperimentsFrom.
List<Experiment>	AbstractXmlModelledInteractionWriter.extractDefaultExperimentsFrom(I interaction)	extractDefaultExperimentsFrom.
List<Experiment>	AbstractXmlInteractionWriter.getDefaultExperiments()	The default experiments that will be used to write a valid XML file but are not real experiments attached to the interaction.

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

Modifier and Type	Method	Description
CvTerm	XmlExperimentWriter.extractDefaultParticipantIdentificationMethod(Experiment exp)	extractDefaultParticipantIdentificationMethod.
void	AbstractXmlModelledInteractionWriter.setDefaultExperiment(Experiment defaultExperiment)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
protected void	XmlExperimentWriter.writeHostOrganism(Experiment object)	writeHostOrganism.
protected void	XmlExperimentWriter.writeOtherProperties(Experiment object)	writeOtherProperties.
protected CvTerm	XmlExperimentWriter.writeParticipantIdentificationMethod(Experiment object)	writeParticipantIdentificationMethod.

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

Modifier and Type	Method	Description
void	AbstractXmlInteractionWriter.setDefaultExperiments(List<Experiment> exp)	Sets the default experiments that will be used to write a valid XML file even if the interaction does not have any valid experiment

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

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

Modifier and Type	Method	Description
List<Experiment>	AbstractXmlModelledInteractionWriter.extractDefaultExperimentsFrom(I interaction)	extractDefaultExperimentsFrom.
List<Experiment>	AbstractXmlModelledInteractionWriter.getDefaultExperiments()	The default experiments that will be used to write a valid XML file but are not real experiments attached to the interaction.

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

Modifier and Type	Method	Description
CvTerm	XmlExperimentWriter.extractDefaultParticipantIdentificationMethod(Experiment exp)	extractDefaultParticipantIdentificationMethod.
protected void	XmlExperimentWriter.writeHostOrganism(Experiment object)	writeHostOrganism.
protected void	XmlExperimentWriter.writeOtherProperties(Experiment object)	writeOtherProperties.
protected CvTerm	XmlExperimentWriter.writeParticipantIdentificationMethod(Experiment object)	writeParticipantIdentificationMethod.

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

Modifier and Type	Method	Description
void	AbstractXmlModelledInteractionWriter.setDefaultExperiments(List<Experiment> exp)	Sets the default experiments that will be used to write a valid XML file even if the interaction does not have any valid experiment

Uses of Experiment 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 Experiment

Modifier and Type	Method	Description
Experiment	XmlParameterWriter.getDefaultExperiment()	The default experiment that will be used to write a valid XML file but is not a real experiment attached to the interaction.

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

Modifier and Type	Method	Description
protected void	XmlExperimentWriter.writeExperimentXrefs(Experiment object, String imexId)	writeExperimentXrefs.
protected void	XmlNamedExperimentWriter.writeNames(Experiment object)	writeNames.
protected void	XmlExperimentWriter.writeOtherAttributes(Experiment object, boolean needToWriteAttributeList)	writeOtherAttributes.
protected void	XmlExperimentWriter.writeVariableParameters(Experiment object)	writeVariableParameters.
protected void	XmlExperimentWriter.writeXrefFromExperimentXrefs(Experiment object, String imexId)	writeXrefFromExperimentXrefs.

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

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

Modifier and Type	Method	Description
protected void	XmlExperimentWriter.writeExperimentXrefs(Experiment object, String imexId)	writeExperimentXrefs.
protected void	XmlNamedExperimentWriter.writeNames(Experiment object)	writeNames.
protected void	XmlExperimentWriter.writeOtherAttributes(Experiment object, boolean needToWriteAttributeList)	writeOtherAttributes.
protected void	XmlExperimentWriter.writeVariableParameters(Experiment object)	writeVariableParameters.

Uses of Experiment in psidev.psi.mi.jami.xml.listener

Method parameters in psidev.psi.mi.jami.xml.listener with type arguments of type Experiment

Modifier and Type	Method	Description
void	PsiXmlParserCompositeListener.onSeveralExperimentsFound(Collection<Experiment> experiments, FileSourceLocator locator)	onSeveralExperimentsFound.
void	PsiXmlParserListener.onSeveralExperimentsFound(Collection<Experiment> experiments, FileSourceLocator locator)	onSeveralExperimentsFound.
void	PsiXmlParserLogger.onSeveralExperimentsFound(Collection<Experiment> experiments, FileSourceLocator locator)	onSeveralExperimentsFound.

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

Subinterfaces of Experiment in psidev.psi.mi.jami.xml.model.extension

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlExperiment	Extended experiment for PSI-XML 2,5 standards

Fields in psidev.psi.mi.jami.xml.model.extension with type parameters of type Experiment

Modifier and Type	Field	Description
protected List<Experiment>	AbstractInferredInteraction.AbstractJAXBExperimentRefWrapper.experiments

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

Modifier and Type	Method	Description
List<Experiment>	AbstractExperimentalInteractor.AbstractJAXBExperimentRefWrapper.getExperiments()
abstract Collection<Experiment>	AbstractExperimentalInteractor.getExperiments()
List<Experiment>	AbstractInferredInteraction.AbstractJAXBExperimentRefWrapper.getExperiments()
abstract Collection<Experiment>	AbstractInferredInteraction.getExperiments()	getExperiments.
List<Experiment>	ExtendedPsiXmlFeatureEvidence.getExperiments()	getExperiments.
List<Experiment>	ExtendedPsiXmlInteractionEvidence.getExperiments()	getExperiments.
List<Experiment>	ExtendedPsiXmlModelledInteraction.getExperiments()	getExperiments.

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

Modifier and Type	Method	Description
void	AbstractExperimentalInteractor.AbstractJAXBExperimentRefWrapper.setExperiments(List<Experiment> experiments)

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

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

Modifier and Type	Method	Description
Experiment	AbstractXmlBinaryInteractionEvidence.getExperiment()	getExperiment.
Experiment	XmlBinaryInteractionEvidenceWrapper.getExperiment()	The experiment which determined the interaction.

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

Modifier and Type	Method	Description
List<Experiment>	AbstractXmlBinaryInteractionEvidence.getExperiments()	getExperiments.
List<Experiment>	XmlBinaryInteractionEvidenceWrapper.getExperiments()	getExperiments.
List<Experiment>	XmlModelledBinaryInteraction.getExperiments()	getExperiments.
List<Experiment>	XmlModelledBinaryInteractionWrapper.getExperiments()	getExperiments.

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

Modifier and Type	Method	Description
void	AbstractXmlBinaryInteractionEvidence.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	XmlBinaryInteractionEvidenceWrapper.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	AbstractXmlBinaryInteractionEvidence.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	XmlBinaryInteractionEvidenceWrapper.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction

Uses of Experiment in psidev.psi.mi.jami.xml.model.extension.datasource

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

Modifier and Type	Method	Description
void	AbstractPsiXmlStream.onSeveralExperimentsFound(Collection<Experiment> experiments, FileSourceLocator locator)	onSeveralExperimentsFound.
void	DefaultPsiXmlStreamSource.onSeveralExperimentsFound(Collection<Experiment> experiments, FileSourceLocator locator)	onSeveralExperimentsFound.

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

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

Modifier and Type	Class	Description
class	AbstractXmlExperiment	Xml im
class	DefaultXmlExperiment	Xml im
class	XmlExperiment	Xml im

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return Experiment

Modifier and Type	Method	Description
Experiment	AbstractXmlInteractionEvidence.getExperiment()	getExperiment.
Experiment	XmlParameter.getExperiment()	Getter for the field experiment.
Experiment	XmlVariableParameter.getExperiment()	Getter for the field experiment.

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

Modifier and Type	Method	Description
List<Experiment>	AbstractXmlInteractionEvidence.getExperiments()	getExperiments.
List<Experiment>	AbstractXmlModelledInteraction.getExperiments()	getExperiments.
Collection<Experiment>	BibRef.getExperiments()	Getter for the field experiments.
Collection<Experiment>	ExperimentalCvTerm.getExperiments()	getExperiments.
Collection<Experiment>	ExperimentalInteractor.getExperiments()	getExperiments.
Collection<Experiment>	HostOrganism.getExperiments()	getExperiments.
Collection<Experiment>	InferredInteraction.getExperiments()	getExperiments.
Collection<Experiment>	XmlConfidence.getExperiments()	getExperiments.
List<Experiment>	XmlFeatureEvidence.getExperiments()	getExperiments.
List<Experiment>	XmlModelledInteractionComplexWrapper.getExperiments()	getExperiments.
List<Experiment>	AbstractXmlModelledInteraction.JAXBExperimentWrapper.getJAXBExperimentDescriptions()

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

Modifier and Type	Method	Description
boolean	BibRef.addExperiment(Experiment exp)	This method will add the experiment and set the publication of the new experiment to this current publication
boolean	BibRef.removeExperiment(Experiment exp)	This method will remove the experiment and set the publication of the removed experiment to null.
void	AbstractXmlInteractionEvidence.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	XmlParameter.setExperiment(Experiment experiment)	Setter for the field experiment.
void	XmlVariableParameter.setExperiment(Experiment experiment)	Sets the experiment for this variableParameter
void	AbstractXmlInteractionEvidence.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	XmlVariableParameter.setExperimentAndAddVariableParameter(Experiment experiment)	Sets the experiment for this variableParameter and add this variableParameter to the list of variableParameters of this experiment.

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

Modifier and Type	Method	Description
boolean	BibRef.addAllExperiments(Collection<? extends Experiment> exps)	This method will add all the experiments and set the publication of the new experiments to this current publication
boolean	BibRef.removeAllExperiments(Collection<? extends Experiment> exps)	This method will remove the experiments and set the publication of the removed experiments to null.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Experiment

Constructor	Description
XmlCooperativityEvidence(Experiment exp)	Constructor for XmlCooperativityEvidence.
XmlVariableParameter(String description, Experiment experiment)	Constructor for XmlVariableParameter.
XmlVariableParameter(String description, Experiment experiment, CvTerm unit)	Constructor for XmlVariableParameter.

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

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

Modifier and Type	Class	Description
class	AbstractXmlExperiment	Xml im
class	DefaultXmlExperiment	Xml im
class	XmlExperiment	Xml im

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return Experiment

Modifier and Type	Method	Description
Experiment	AbstractXmlInteractionEvidence.getExperiment()	getExperiment.
Experiment	XmlParameter.getExperiment()	Getter for the field experiment.
Experiment	XmlVariableParameter.getExperiment()	Getter for the field experiment.

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

Modifier and Type	Method	Description
List<Experiment>	AbstractXmlInteractionEvidence.getExperiments()	getExperiments.
List<Experiment>	AbstractXmlModelledInteraction.getExperiments()	getExperiments.
Collection<Experiment>	BibRef.getExperiments()	Getter for the field experiments.
Collection<Experiment>	ExperimentalCvTerm.getExperiments()	getExperiments.
Collection<Experiment>	ExperimentalInteractor.getExperiments()	getExperiments.
Collection<Experiment>	HostOrganism.getExperiments()	getExperiments.
Collection<Experiment>	InferredInteraction.getExperiments()	getExperiments.
Collection<Experiment>	XmlConfidence.getExperiments()	getExperiments.
List<Experiment>	XmlFeatureEvidence.getExperiments()	getExperiments.
List<Experiment>	XmlModelledInteractionComplexWrapper.getExperiments()	getExperiments.
List<Experiment>	AbstractXmlModelledInteraction.JAXBExperimentWrapper.getJAXBExperimentDescriptions()

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

Modifier and Type	Method	Description
boolean	BibRef.addExperiment(Experiment exp)	This method will add the experiment and set the publication of the new experiment to this current publication
boolean	BibRef.removeExperiment(Experiment exp)	This method will remove the experiment and set the publication of the removed experiment to null.
void	AbstractXmlInteractionEvidence.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	XmlParameter.setExperiment(Experiment experiment)	Setter for the field experiment.
void	XmlVariableParameter.setExperiment(Experiment experiment)	Sets the experiment for this variableParameter
void	AbstractXmlInteractionEvidence.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	XmlVariableParameter.setExperimentAndAddVariableParameter(Experiment experiment)	Sets the experiment for this variableParameter and add this variableParameter to the list of variableParameters of this experiment.

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

Modifier and Type	Method	Description
boolean	BibRef.addAllExperiments(Collection<? extends Experiment> exps)	This method will add all the experiments and set the publication of the new experiments to this current publication
boolean	BibRef.removeAllExperiments(Collection<? extends Experiment> exps)	This method will remove the experiments and set the publication of the removed experiments to null.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Experiment

Constructor	Description
XmlCooperativityEvidence(Experiment exp)	Constructor for XmlCooperativityEvidence.
XmlVariableParameter(String description, Experiment experiment)	Constructor for XmlVariableParameter.
XmlVariableParameter(String description, Experiment experiment, CvTerm unit)	Constructor for XmlVariableParameter.

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

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

Modifier and Type	Class	Description
class	AbstractXmlExperiment	Xml im
class	DefaultXmlExperiment	Xml im
class	XmlExperiment	Xml 3.0 implementation of experiment

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return Experiment

Modifier and Type	Method	Description
Experiment	AbstractXmlInteractionEvidence.getExperiment()	getExperiment.
Experiment	XmlParameter.getExperiment()	Getter for the field experiment.
Experiment	XmlVariableParameter.getExperiment()	Getter for the field experiment.

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

Modifier and Type	Method	Description
List<Experiment>	AbstractXmlInteractionEvidence.getExperiments()	getExperiments.
List<Experiment>	AbstractXmlModelledInteraction.getExperiments()	getExperiments.
Collection<Experiment>	BibRef.getExperiments()	Getter for the field experiments.
Collection<Experiment>	ExperimentalCvTerm.getExperiments()	getExperiments.
Collection<Experiment>	ExperimentalInteractor.getExperiments()	getExperiments.
Collection<Experiment>	HostOrganism.getExperiments()	getExperiments.
Collection<Experiment>	InferredInteraction.getExperiments()	getExperiments.
Collection<Experiment>	XmlConfidence.getExperiments()	getExperiments.
List<Experiment>	XmlFeatureEvidence.getExperiments()	getExperiments.
List<Experiment>	XmlModelledInteractionComplexWrapper.getExperiments()	getExperiments.
List<Experiment>	AbstractXmlModelledInteraction.JAXBExperimentWrapper.getJAXBExperimentDescriptions()

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

Modifier and Type	Method	Description
boolean	BibRef.addExperiment(Experiment exp)	This method will add the experiment and set the publication of the new experiment to this current publication
boolean	BibRef.removeExperiment(Experiment exp)	This method will remove the experiment and set the publication of the removed experiment to null.
void	AbstractXmlInteractionEvidence.setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	XmlParameter.setExperiment(Experiment experiment)	Setter for the field experiment.
void	XmlVariableParameter.setExperiment(Experiment experiment)	Sets the experiment for this variableParameter
void	AbstractXmlInteractionEvidence.setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	XmlVariableParameter.setExperimentAndAddVariableParameter(Experiment experiment)	Sets the experiment for this variableParameter and add this variableParameter to the list of variableParameters of this experiment.

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

Modifier and Type	Method	Description
boolean	BibRef.addAllExperiments(Collection<? extends Experiment> exps)	This method will add all the experiments and set the publication of the new experiments to this current publication
boolean	BibRef.removeAllExperiments(Collection<? extends Experiment> exps)	This method will remove the experiments and set the publication of the removed experiments to null.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Experiment

Constructor	Description
XmlVariableParameter(String description, Experiment experiment)	Constructor for XmlVariableParameter.
XmlVariableParameter(String description, Experiment experiment, CvTerm unit)	Constructor for XmlVariableParameter.

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

Classes in psidev.psi.mi.jami.xml.model.reference.xml253 that implement Experiment

Modifier and Type	Class	Description
class	AbstractExperimentRef	Abstract class for an ModelledInteractionRef

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

Classes in psidev.psi.mi.jami.xml.model.reference.xml254 that implement Experiment

Modifier and Type	Class	Description
class	AbstractExperimentRef	Abstract class for an ModelledInteractionRef

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

Classes in psidev.psi.mi.jami.xml.model.reference.xml300 that implement Experiment

Modifier and Type	Class	Description
class	AbstractExperimentRef	Abstract class for an ModelledInteractionRef

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

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

Modifier and Type	Method	Description
List<Experiment>	ComplexEntry.getExperiments()	getExperiments.
List<Experiment>	ExperimentalEntry.getExperiments()	getExperiments.
List<Experiment>	ModelledEntry.getExperiments()	getExperiments.
List<Experiment>	ComplexEntry.JAXBExperimentsWrapper.getJAXBExperiments()
List<Experiment>	ExperimentalEntry.JAXBExperimentsWrapper.getJAXBExperiments()
List<Experiment>	ModelledEntry.JAXBExperimentsWrapper.getJAXBExperiments()

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

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

Modifier and Type	Method	Description
List<Experiment>	ComplexEntry.getExperiments()	getExperiments.
List<Experiment>	ExperimentalEntry.getExperiments()	getExperiments.
List<Experiment>	ModelledEntry.getExperiments()	getExperiments.
List<Experiment>	ComplexEntry.JAXBExperimentsWrapper.getJAXBExperiments()
List<Experiment>	ExperimentalEntry.JAXBExperimentsWrapper.getJAXBExperiments()
List<Experiment>	ModelledEntry.JAXBExperimentsWrapper.getJAXBExperiments()

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

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

Modifier and Type	Method	Description
List<Experiment>	ComplexEntry.getExperiments()	getExperiments.
List<Experiment>	Entry.getExperiments()	getExperiments.
List<Experiment>	ExperimentalEntry.getExperiments()	getExperiments.
List<Experiment>	ModelledEntry.getExperiments()	getExperiments.
List<Experiment>	ComplexEntry.JAXBExperimentsWrapper.getJAXBExperiments()
List<Experiment>	Entry.JAXBExperimentsWrapper.getJAXBExperiments()
List<Experiment>	ExperimentalEntry.JAXBExperimentsWrapper.getJAXBExperiments()
List<Experiment>	ModelledEntry.JAXBExperimentsWrapper.getJAXBExperiments()