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

Packages that use InteractionEvidence

Package	Description
psidev.psi.mi.jami.binary
psidev.psi.mi.jami.binary.expansion
psidev.psi.mi.jami.binary.impl
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.crosslink.extension.datasource
psidev.psi.mi.jami.crosslink.io.iterator
psidev.psi.mi.jami.crosslink.io.parser
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.factory
psidev.psi.mi.jami.html
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.json.binary
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.extension.datasource
psidev.psi.mi.jami.tab.io.iterator
psidev.psi.mi.jami.tab.io.parser
psidev.psi.mi.jami.tab.io.writer
psidev.psi.mi.jami.tab.io.writer.extended
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator.interaction
psidev.psi.mi.jami.xml.io.iterator
psidev.psi.mi.jami.xml.io.parser
psidev.psi.mi.jami.xml.io.writer.compact
psidev.psi.mi.jami.xml.io.writer.compact.extended
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.abstracts.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml30
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.expanded
psidev.psi.mi.jami.xml.model.extension
psidev.psi.mi.jami.xml.model.extension.binary
psidev.psi.mi.jami.xml.model.extension.binary.xml253
psidev.psi.mi.jami.xml.model.extension.binary.xml254
psidev.psi.mi.jami.xml.model.extension.binary.xml30
psidev.psi.mi.jami.xml.model.extension.datasource
psidev.psi.mi.jami.xml.model.extension.factory.xml25
psidev.psi.mi.jami.xml.model.extension.factory.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.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 InteractionEvidence in psidev.psi.mi.jami.binary

Subinterfaces of InteractionEvidence in psidev.psi.mi.jami.binary

Modifier and Type	Interface	Description
interface	BinaryInteractionEvidence	A BinaryInteractionEvidence is an InteractionEvidence with only two participants

Uses of InteractionEvidence in psidev.psi.mi.jami.binary.expansion

Methods in psidev.psi.mi.jami.binary.expansion with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected ParticipantEvidence	InteractionEvidenceSpokeExpansion.collectBestBaitForSpokeExpansion(InteractionEvidence interaction)	collectBestBaitForSpokeExpansion
protected Collection<BinaryInteractionEvidence>	InteractionEvidenceBipartiteExpansion.collectBinaryInteractionsFromNary(InteractionEvidence interaction)	collectBinaryInteractionsFromNary
protected <P extends Participant> BinaryInteractionEvidence	InteractionEvidenceBipartiteExpansion.createBinaryInteraction(InteractionEvidence interaction, P c1, P c2)	createBinaryInteraction
protected <P extends Participant> BinaryInteractionEvidence	InteractionEvidenceMatrixExpansion.createBinaryInteraction(InteractionEvidence interaction, P c1, P c2)	createBinaryInteraction
protected <P extends Participant> BinaryInteractionEvidence	InteractionEvidenceSpokeExpansion.createBinaryInteraction(InteractionEvidence interaction, P c1, P c2)	createBinaryInteraction
protected Collection<BinaryInteractionEvidence>	InteractionEvidenceBipartiteExpansion.createBinaryInteractionWrappersFrom(InteractionEvidence interaction)	createBinaryInteractionWrappersFrom
protected Collection<BinaryInteractionEvidence>	InteractionEvidenceMatrixExpansion.createBinaryInteractionWrappersFrom(InteractionEvidence interaction)	createBinaryInteractionWrappersFrom
protected Collection<BinaryInteractionEvidence>	InteractionEvidenceSpokeExpansion.createBinaryInteractionWrappersFrom(InteractionEvidence interaction)	createBinaryInteractionWrappersFrom
protected Collection<BinaryInteractionEvidence>	InteractionEvidenceBipartiteExpansion.createNewSelfBinaryInteractionsFrom(InteractionEvidence interaction)	createNewSelfBinaryInteractionsFrom
protected Collection<BinaryInteractionEvidence>	InteractionEvidenceMatrixExpansion.createNewSelfBinaryInteractionsFrom(InteractionEvidence interaction)	createNewSelfBinaryInteractionsFrom
protected Collection<BinaryInteractionEvidence>	InteractionEvidenceSpokeExpansion.createNewSelfBinaryInteractionsFrom(InteractionEvidence interaction)	createNewSelfBinaryInteractionsFrom
protected ParticipantEvidence[]	InteractionEvidenceMatrixExpansion.createParticipantsArray(InteractionEvidence interaction)	createParticipantsArray
protected ComplexType	InteractionEvidenceBipartiteExpansion.findInteractionCategory(InteractionEvidence interaction)	findInteractionCategory
protected ComplexType	InteractionEvidenceMatrixExpansion.findInteractionCategory(InteractionEvidence interaction)	findInteractionCategory
protected ComplexType	InteractionEvidenceSpokeExpansion.findInteractionCategory(InteractionEvidence interaction)	findInteractionCategory

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

Classes in psidev.psi.mi.jami.binary.impl that implement InteractionEvidence

Modifier and Type	Class	Description
class	BinaryInteractionEvidenceWrapper	A wrapper for InteractionEvidence which contains two participants
class	DefaultBinaryInteractionEvidence	Default implementation for BinaryInteractionEvidence
class	DefaultNamedBinaryInteractionEvidence	Default implementation of a Named binary interaction evidence

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

Modifier and Type	Method	Description
Collection<InteractionEvidence>	DefaultModelledBinaryInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	ModelledBinaryInteractionWrapper.getInteractionEvidences()	getInteractionEvidences

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

Modifier and Type	Method	Description
protected void	DefaultModelledBinaryInteraction.initialiseInteractionEvidencesWith(Collection<InteractionEvidence> evidences)	initialiseInteractionEvidencesWith

Constructors in psidev.psi.mi.jami.binary.impl with parameters of type InteractionEvidence

Constructor	Description
BinaryInteractionEvidenceWrapper(InteractionEvidence interaction)	Constructor for BinaryInteractionEvidenceWrapper.
BinaryInteractionEvidenceWrapper(InteractionEvidence interaction, CvTerm complexExpansion)	Constructor for BinaryInteractionEvidenceWrapper.

Uses of InteractionEvidence in psidev.psi.mi.jami.crosslink.extension

Subinterfaces of InteractionEvidence in psidev.psi.mi.jami.crosslink.extension

Modifier and Type	Interface	Description
interface	CrosslinkCsvInteraction	Interaction evidence extension from crosslinking CSV files

Classes in psidev.psi.mi.jami.crosslink.extension that implement InteractionEvidence

Modifier and Type	Class	Description
class	CsvBinaryInteractionEvidence	Crosslink CSV implementation of BinaryInteractionEvidence
class	CsvInteractionEvidence	CSV extension for InteractionEvidence

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

Constructor	Description
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.

Uses of InteractionEvidence in psidev.psi.mi.jami.crosslink.extension.datasource

Classes in psidev.psi.mi.jami.crosslink.extension.datasource with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	AbstractCsvSource<T extends InteractionEvidence>	Abstract class for an InteractionSource coming from a Crosslink CSV file.
class	AbstractCsvStreamSource<T extends InteractionEvidence>	abstract class for Crosslink Csv datasource.
interface	CsvSource<I extends InteractionEvidence>	Interface for Crosslink CSV sources that can parse full CSV files
interface	CsvStreamSource<I extends InteractionEvidence>	Interface for Crosslink CSV datasources that can stream CSV files

Methods in psidev.psi.mi.jami.crosslink.extension.datasource that return types with arguments of type InteractionEvidence

Modifier and Type	Method	Description
Collection<InteractionEvidence>	CsvMixedEvidenceSource.getInteractions()	getInteractions.
Collection<InteractionEvidence>	CsvNaryEvidenceSource.getInteractions()	getInteractions.
Iterator<InteractionEvidence>	CsvMixedEvidenceSource.getInteractionsIterator()	getInteractionsIterator.
Iterator<InteractionEvidence>	CsvNaryEvidenceSource.getInteractionsIterator()	getInteractionsIterator.
protected AbstractCsvInteractionEvidenceParser<InteractionEvidence>	CsvEvidenceSource.instantiateLineParser()	instantiateLineParser.
protected AbstractCsvInteractionEvidenceParser<InteractionEvidence>	CsvEvidenceStreamSource.instantiateLineParser()	instantiateLineParser.

Uses of InteractionEvidence in psidev.psi.mi.jami.crosslink.io.iterator

Classes in psidev.psi.mi.jami.crosslink.io.iterator with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	CsvInteractionEvidenceIterator<T extends InteractionEvidence>	Crosslink CSV interaction evidence iterator

Uses of InteractionEvidence in psidev.psi.mi.jami.crosslink.io.parser

Classes in psidev.psi.mi.jami.crosslink.io.parser with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	AbstractCsvInteractionEvidenceParser<T extends InteractionEvidence>	Abstract class for crosslink CSV parser

Methods in psidev.psi.mi.jami.crosslink.io.parser that return InteractionEvidence

Modifier and Type	Method	Description
protected InteractionEvidence	CsvInteractionEvidenceParser.instantiateInteractionEvidence(int linePosition, String bait)	instantiateInteractionEvidence.

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

Classes in psidev.psi.mi.jami.datasource with type parameters of type InteractionEvidence

Modifier and Type	Interface	Description
interface	InteractionEvidenceSource<T extends InteractionEvidence>	A Data source of interaction evidences.
interface	InteractionEvidenceStream<T extends InteractionEvidence>	A Data source of interaction evidences giving only a stream of interactions.

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

Methods in psidev.psi.mi.jami.enricher.impl.full that return types with arguments of type InteractionEvidence

Modifier and Type	Method	Description
protected FullInteractionEnricher<InteractionEvidence>	FullInteractionEvidenceEnricher.getInteractionEnricher()	Getter for the field interactionEnricher.
InteractionEnricherListener<InteractionEvidence>	FullInteractionEvidenceEnricher.getInteractionEnricherListener()	The listener for changes made to interactions.

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

Modifier and Type	Method	Description
protected void	FullInteractionEvidenceEnricher.mergerVariableParameters(InteractionEvidence interactionToEnrich, InteractionEvidence objectSource, boolean remove)	mergerVariableParameters.
protected void	FullInteractionEvidenceEnricher.processConfidences(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processConfidences.
protected void	FullInteractionEvidenceUpdater.processConfidences(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processConfidences.
protected void	FullInteractionEvidenceUpdater.processExperiment(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processExperiment.
protected void	FullInteractionEvidenceEnricher.processOtherProperties(InteractionEvidence interactionToEnrich)	The strategy used for enriching the interaction.
protected void	FullInteractionEvidenceEnricher.processOtherProperties(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processOtherProperties.
protected void	FullInteractionEvidenceUpdater.processOtherProperties(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processOtherProperties.
protected void	FullInteractionEvidenceEnricher.processParameters(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processParameters.
protected void	FullInteractionEvidenceUpdater.processParameters(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processParameters.
protected void	FullInteractionEvidenceEnricher.processVariableParameters(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processVariableParameters.
protected void	FullInteractionEvidenceUpdater.processVariableParameters(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processVariableParameters.

Constructor parameters in psidev.psi.mi.jami.enricher.impl.full with type arguments of type InteractionEvidence

Constructor	Description
FullInteractionEvidenceEnricher(FullInteractionEnricher<InteractionEvidence> interactionEnricher)	Constructor for FullInteractionEvidenceEnricher.
FullInteractionEvidenceUpdater(FullInteractionUpdater<InteractionEvidence> interactionEnricher)	Constructor for FullInteractionEvidenceUpdater.

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

Methods in psidev.psi.mi.jami.enricher.impl.minimal that return types with arguments of type InteractionEvidence

Modifier and Type	Method	Description
MinimalInteractionUpdater<InteractionEvidence>	MinimalInteractionEvidenceUpdater.getDelegate()	Getter for the field delegate.
InteractionEnricherListener<InteractionEvidence>	MinimalInteractionEvidenceUpdater.getInteractionEnricherListener()	The listener for changes made to interactions.

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

Modifier and Type	Method	Description
protected void	MinimalInteractionEvidenceEnricher.processExperiment(InteractionEvidence interactionToEnrich)	processExperiment.
protected void	MinimalInteractionEvidenceEnricher.processExperiment(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processExperiment.
protected void	MinimalInteractionEvidenceUpdater.processExperiment(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processExperiment.
void	MinimalInteractionEvidenceUpdater.processMinimalUpdates(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processMinimalUpdates.
protected void	MinimalInteractionEvidenceEnricher.processOtherProperties(InteractionEvidence interactionToEnrich)	The strategy used for enriching the interaction.
protected void	MinimalInteractionEvidenceEnricher.processOtherProperties(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processOtherProperties.
protected void	MinimalInteractionEvidenceUpdater.processOtherProperties(InteractionEvidence objectToEnrich, InteractionEvidence objectSource)	processOtherProperties.

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

Modifier and Type	Method	Description
void	MinimalInteractionEvidenceUpdater.setInteractionEnricherListener(InteractionEnricherListener<InteractionEvidence> listener)	setInteractionEnricherListener.

Constructor parameters in psidev.psi.mi.jami.enricher.impl.minimal with type arguments of type InteractionEvidence

Constructor	Description
MinimalInteractionEvidenceUpdater(MinimalInteractionUpdater<InteractionEvidence> delegate)	Constructor for MinimalInteractionEvidenceUpdater.

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

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

Modifier and Type	Method	Description
void	InteractionEvidenceEnricherListenerManager.onAddedConfidence(InteractionEvidence o, Confidence added)	Listen to the event where a confidence has been added to the object confidences.
void	ModelledInteractionEnricherListenerManager.onAddedInteractionEvidence(I interaction, InteractionEvidence added)	onAddedInteractionEvidence
void	InteractionEvidenceEnricherListenerManager.onAddedParameter(InteractionEvidence o, Parameter added)	Listen to the event where a parameter has been added to the object parameters.
void	InteractionEvidenceEnricherListenerManager.onAddedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet added)	onAddedVariableParameterValues
void	InteractionEvidenceEnricherListenerManager.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	InteractionEvidenceEnricherListenerManager.onInferredPropertyUpdate(InteractionEvidence interaction, boolean oldInferred)	onInferredPropertyUpdate
void	InteractionEvidenceEnricherListenerManager.onNegativePropertyUpdate(InteractionEvidence interaction, boolean negative)	onNegativePropertyUpdate
void	InteractionEvidenceEnricherListenerManager.onRemovedConfidence(InteractionEvidence o, Confidence removed)	Listen to the event where a confidence has been removed from the object confidences.
void	ModelledInteractionEnricherListenerManager.onRemovedInteractionEvidence(I interaction, InteractionEvidence removed)	onRemovedInteractionEvidence
void	InteractionEvidenceEnricherListenerManager.onRemovedParameter(InteractionEvidence o, Parameter removed)	Listen to the event where a parameter has been removed from the object parameters.
void	InteractionEvidenceEnricherListenerManager.onRemovedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet removed)	onRemovedVariableParameterValues

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

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

Modifier and Type	Method	Description
void	InteractionEvidenceEnricherLogger.onEnrichmentComplete(InteractionEvidence interaction, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	InteractionEvidenceEnricherLogger.onEnrichmentError(InteractionEvidence object, String message, Exception e)	onEnrichmentError.

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

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

Modifier and Type	Method	Description
void	InteractionEvidenceEnricherStatisticsWriter.onAddedConfidence(InteractionEvidence o, Confidence added)	Listen to the event where a confidence has been added to the object confidences.
void	ModelledInteractionEnricherStatisticsWriter.onAddedInteractionEvidence(I interaction, InteractionEvidence added)	onAddedInteractionEvidence
void	InteractionEvidenceEnricherStatisticsWriter.onAddedParameter(InteractionEvidence o, Parameter added)	Listen to the event where a parameter has been added to the object parameters.
void	InteractionEvidenceEnricherStatisticsWriter.onAddedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet added)	onAddedVariableParameterValues
void	InteractionEvidenceEnricherStatisticsWriter.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	InteractionEvidenceEnricherStatisticsWriter.onInferredPropertyUpdate(InteractionEvidence interaction, boolean oldInferred)	onInferredPropertyUpdate
void	InteractionEvidenceEnricherStatisticsWriter.onNegativePropertyUpdate(InteractionEvidence interaction, boolean negative)	onNegativePropertyUpdate
void	InteractionEvidenceEnricherStatisticsWriter.onRemovedConfidence(InteractionEvidence o, Confidence removed)	Listen to the event where a confidence has been removed from the object confidences.
void	ModelledInteractionEnricherStatisticsWriter.onRemovedInteractionEvidence(I interaction, InteractionEvidence removed)	onRemovedInteractionEvidence
void	InteractionEvidenceEnricherStatisticsWriter.onRemovedParameter(InteractionEvidence o, Parameter removed)	Listen to the event where a parameter has been removed from the object parameters.
void	InteractionEvidenceEnricherStatisticsWriter.onRemovedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet removed)	onRemovedVariableParameterValues

Uses of InteractionEvidence in psidev.psi.mi.jami.factory

Methods in psidev.psi.mi.jami.factory with parameters of type InteractionEvidence

Modifier and Type	Method	Description
BinaryInteractionEvidence	BinaryInteractionFactory.createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)	Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidences
BinaryInteractionEvidence	DefaultBinaryInteractionFactory.createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)	Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidences
BinaryInteractionEvidence	BinaryInteractionFactory.createBinaryInteractionEvidenceWrapperFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence that wraps the given interaction
BinaryInteractionEvidence	DefaultBinaryInteractionFactory.createBinaryInteractionEvidenceWrapperFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence that wraps the given interaction
BinaryInteractionEvidence	BinaryInteractionFactory.createSelfBinaryInteractionEvidenceFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence representing a self interaction
BinaryInteractionEvidence	DefaultBinaryInteractionFactory.createSelfBinaryInteractionEvidenceFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence representing a self interaction

Uses of InteractionEvidence in psidev.psi.mi.jami.html

Methods in psidev.psi.mi.jami.html with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected void	MIEvidenceHtmlWriter.writeConfidences(InteractionEvidence interaction)	writeConfidences
protected void	MIEvidenceHtmlWriter.writeCooperativeEffects(InteractionEvidence interaction)	writeCooperativeEffects
protected void	MIEvidenceHtmlWriter.writeExperiment(InteractionEvidence interaction)	writeExperiment
protected void	MIEvidenceHtmlWriter.writeGeneralProperties(InteractionEvidence interaction)	writeGeneralProperties
protected void	MIEvidenceHtmlWriter.writeParameters(InteractionEvidence interaction)	writeParameters

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

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

Modifier and Type	Method	Description
boolean	ImexAssigner.isEntitledToImex(InteractionEvidence interaction)	isEntitledToImex.
boolean	ImexAssigner.updateImexIdentifierForInteraction(InteractionEvidence interaction, String imexId)	Add a IMEx primary reference to the interaction

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

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

Modifier and Type	Method	Description
boolean	ImexAssignerImpl.isEntitledToImex(InteractionEvidence interaction)	isEntitledToImex.
boolean	ImexAssignerImpl.updateImexIdentifierForInteraction(InteractionEvidence interaction, String imexId)	Add a IMEx primary reference to the interaction

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

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

Modifier and Type	Method	Description
void	InteractionImexEnricherListener.onImexIdAssigned(InteractionEvidence interaction, String imex)	onImexIdAssigned.
void	InteractionImexEnricherListener.onImexIdConflicts(InteractionEvidence originalInteraction, Collection<Xref> conflictingXrefs)	onImexIdConflicts.

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

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

Modifier and Type	Method	Description
void	InteractionEvidenceImexEnricherListenerManager.onImexIdAssigned(InteractionEvidence interaction, String imex)	onImexIdAssigned.
void	InteractionEvidenceImexEnricherLogger.onImexIdAssigned(InteractionEvidence interaction, String imex)	onImexIdAssigned.
void	InteractionEvidenceImexEnricherStatisticsWriter.onImexIdAssigned(InteractionEvidence interaction, String imex)	onImexIdAssigned.
void	InteractionEvidenceImexEnricherListenerManager.onImexIdConflicts(InteractionEvidence originalInteraction, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	InteractionEvidenceImexEnricherLogger.onImexIdConflicts(InteractionEvidence interactionEvidence, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	InteractionEvidenceImexEnricherStatisticsWriter.onImexIdConflicts(InteractionEvidence interaction, Collection<Xref> conflictingXrefs)	onImexIdConflicts.

Uses of InteractionEvidence in psidev.psi.mi.jami.json.binary

Constructor parameters in psidev.psi.mi.jami.json.binary with type arguments of type InteractionEvidence

Constructor	Description
MIJsonEvidenceWriter(File file, OntologyTermFetcher fetcher, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for MIJsonEvidenceWriter.
MIJsonEvidenceWriter(OutputStream output, OntologyTermFetcher fetcher, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for MIJsonEvidenceWriter.
MIJsonEvidenceWriter(Writer writer, OntologyTermFetcher fetcher, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for MIJsonEvidenceWriter.

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

Classes in psidev.psi.mi.jami.json.elements with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	SimpleJsonInteractionEvidenceWriter<I extends InteractionEvidence>	Json writer for interaction evidences

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

Modifier and Type	Method	Description
JsonElementWriter<InteractionEvidence>	SimpleJsonInteractionEvidenceWriter.getExperimentWriter()	Getter for the field experimentWriter.

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

Modifier and Type	Method	Description
void	SimpleJsonExperimentWriter.write(InteractionEvidence object)	write.

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

Modifier and Type	Method	Description
void	SimpleJsonInteractionEvidenceWriter.setExperimentWriter(JsonElementWriter<InteractionEvidence> experimentWriter)	Setter for the field experimentWriter.

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

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

Modifier and Type	Method	Description
void	ModelledInteractionChangeListener.onAddedInteractionEvidence(I interaction, InteractionEvidence added)	onAddedInteractionEvidence
void	InteractionEvidenceChangeListener.onAddedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet added)	onAddedVariableParameterValues
void	InteractionEvidenceChangeListener.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	InteractionEvidenceChangeListener.onInferredPropertyUpdate(InteractionEvidence interaction, boolean oldInferred)	onInferredPropertyUpdate
void	InteractionEvidenceChangeListener.onNegativePropertyUpdate(InteractionEvidence interaction, boolean negative)	onNegativePropertyUpdate
void	ModelledInteractionChangeListener.onRemovedInteractionEvidence(I interaction, InteractionEvidence removed)	onRemovedInteractionEvidence
void	InteractionEvidenceChangeListener.onRemovedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet removed)	onRemovedVariableParameterValues

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

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

Modifier and Type	Method	Description
void	InteractionEvidenceChangeLogger.onAddedConfidence(InteractionEvidence o, Confidence added)	Listen to the event where a confidence has been added to the object confidences.
void	ComplexChangeLogger.onAddedInteractionEvidence(Complex interaction, InteractionEvidence added)	onAddedInteractionEvidence
void	ModelledInteractionChangeLogger.onAddedInteractionEvidence(I interaction, InteractionEvidence added)	onAddedInteractionEvidence
void	InteractionEvidenceChangeLogger.onAddedParameter(InteractionEvidence o, Parameter added)	Listen to the event where a parameter has been added to the object parameters.
void	InteractionEvidenceChangeLogger.onAddedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet added)	onAddedVariableParameterValues
void	InteractionEvidenceChangeLogger.onExperimentUpdate(InteractionEvidence interaction, Experiment oldExperiment)	onExperimentUpdate
void	InteractionEvidenceChangeLogger.onInferredPropertyUpdate(InteractionEvidence interaction, boolean oldInferred)	onInferredPropertyUpdate
void	InteractionEvidenceChangeLogger.onNegativePropertyUpdate(InteractionEvidence interaction, boolean oldNegative)	onNegativePropertyUpdate
void	InteractionEvidenceChangeLogger.onRemovedConfidence(InteractionEvidence o, Confidence removed)	Listen to the event where a confidence has been removed from the object confidences.
void	ComplexChangeLogger.onRemovedInteractionEvidence(Complex interaction, InteractionEvidence removed)	onRemovedInteractionEvidence
void	ModelledInteractionChangeLogger.onRemovedInteractionEvidence(I interaction, InteractionEvidence removed)	onRemovedInteractionEvidence
void	InteractionEvidenceChangeLogger.onRemovedParameter(InteractionEvidence o, Parameter removed)	Listen to the event where a parameter has been removed from the object parameters.
void	InteractionEvidenceChangeLogger.onRemovedVariableParameterValues(InteractionEvidence interaction, VariableParameterValueSet removed)	onRemovedVariableParameterValues

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

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

Modifier and Type	Method	Description
<I extends InteractionEvidence> Collection<I>	Experiment.getInteractionEvidences()	The interactions determined in this experiment.
<I extends InteractionEvidence> Collection<I>	ModelledInteraction.getInteractionEvidences()	Interaction evidences supporting this modelled interaction.

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

Modifier and Type	Method	Description
boolean	Experiment.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	Experiment.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

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

Modifier and Type	Method	Description
boolean	Experiment.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	Experiment.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

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

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

Modifier and Type	Class	Description
class	DefaultInteractionEvidence	Default implementation for InteractionEvidence Notes: The equals and hashcode methods have NOT been overridden because the InteractionEvidence object is a complex object.
class	DefaultNamedInteractionEvidence	Default implementation for Named InteractionEvidence

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

Modifier and Type	Method	Description
Collection<InteractionEvidence>	DefaultComplex.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	DefaultExperiment.getInteractionEvidences()	getInteractionEvidences
Collection<InteractionEvidence>	DefaultModelledInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.

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

Modifier and Type	Method	Description
boolean	DefaultExperiment.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	DefaultExperiment.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

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

Modifier and Type	Method	Description
boolean	DefaultExperiment.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
protected void	DefaultComplex.initialiseInteractionEvidencesWith(Collection<InteractionEvidence> interactionEvidences)	initialiseInteractionEvidencesWith
protected void	DefaultModelledInteraction.initialiseInteractionEvidencesWith(Collection<InteractionEvidence> evidences)	initialiseInteractionEvidencesWith
protected void	DefaultExperiment.initialiseInteractionsWith(Collection<InteractionEvidence> interactionEvidences)	initialiseInteractionsWith
boolean	DefaultExperiment.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

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

Constructor	Description
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultExperimentalParticipantPool.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultNamedParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.
DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for DefaultParticipantEvidence.

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

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

Modifier and Type	Class	Description
class	MitabBinaryInteractionEvidence	TODO comment this
class	MitabInteractionEvidence	Mitab extension for InteractionEvidence

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

Constructor	Description
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.
MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for MitabParticipantEvidence.

Uses of InteractionEvidence in psidev.psi.mi.jami.tab.extension.datasource

Methods in psidev.psi.mi.jami.tab.extension.datasource that return types with arguments of type InteractionEvidence

Modifier and Type	Method	Description
protected Iterator<InteractionEvidence>	MitabEvidenceStreamSource.createMitabIterator()	createMitabIterator.

Uses of InteractionEvidence in psidev.psi.mi.jami.tab.io.iterator

Constructor parameters in psidev.psi.mi.jami.tab.io.iterator with type arguments of type InteractionEvidence

Constructor	Description
MitabInteractionEvidenceIterator(MitabLineParser<InteractionEvidence,ParticipantEvidence,FeatureEvidence> lineParser)	Constructor for MitabInteractionEvidenceIterator.

Uses of InteractionEvidence in psidev.psi.mi.jami.tab.io.parser

Classes in psidev.psi.mi.jami.tab.io.parser with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	AbstractInteractionEvidenceLineParser<T extends InteractionEvidence>	Abstract class for Interaction evidence parsers

Methods in psidev.psi.mi.jami.tab.io.parser that return InteractionEvidence

Modifier and Type	Method	Description
protected InteractionEvidence	InteractionEvidenceLineParser.createInteraction()	createInteraction.

Uses of InteractionEvidence in psidev.psi.mi.jami.tab.io.writer

Method parameters in psidev.psi.mi.jami.tab.io.writer with type arguments of type InteractionEvidence

Modifier and Type	Method	Description
protected void	Mitab25EvidenceWriter.initialiseExpansionMethod(ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	initialiseExpansionMethod.

Constructor parameters in psidev.psi.mi.jami.tab.io.writer with type arguments of type InteractionEvidence

Constructor	Description
Mitab25EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab25EvidenceWriter.
Mitab25EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab25EvidenceWriter.
Mitab25EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab25EvidenceWriter.
Mitab26EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab26EvidenceWriter.
Mitab26EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab26EvidenceWriter.
Mitab26EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab26EvidenceWriter.
Mitab27EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab27EvidenceWriter.
Mitab27EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab27EvidenceWriter.
Mitab27EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab27EvidenceWriter.
Mitab28EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab28EvidenceWriter.
Mitab28EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab28EvidenceWriter.
Mitab28EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab28EvidenceWriter.

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

Method parameters in psidev.psi.mi.jami.tab.io.writer.extended with type arguments of type InteractionEvidence

Modifier and Type	Method	Description
protected void	Mitab25EvidenceWriter.initialiseExpansionMethod(ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	initialiseExpansionMethod.

Constructor parameters in psidev.psi.mi.jami.tab.io.writer.extended with type arguments of type InteractionEvidence

Constructor	Description
Mitab25EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab25EvidenceWriter.
Mitab25EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab25EvidenceWriter.
Mitab25EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab25EvidenceWriter.
Mitab26EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab26EvidenceWriter.
Mitab26EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab26EvidenceWriter.
Mitab26EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab26EvidenceWriter.
Mitab27EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab27EvidenceWriter.
Mitab27EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab27EvidenceWriter.
Mitab27EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab27EvidenceWriter.
Mitab28EvidenceWriter(File file, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab28EvidenceWriter.
Mitab28EvidenceWriter(OutputStream output, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab28EvidenceWriter.
Mitab28EvidenceWriter(Writer writer, ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence> expansionMethod)	Constructor for Mitab28EvidenceWriter.

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

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

Modifier and Type	Method	Description
static InteractionEvidence	InteractionUtils.createEmptyBasicExperimentalInteraction()	createEmptyBasicExperimentalInteraction

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

Modifier and Type	Method	Description
static BinaryInteractionEvidence	InteractionUtils.createAndAddNewSelfBinaryInteractionEvidence(InteractionEvidence interaction)	Creates a new BinaryInteractionEvidence from the given interactionEvidence which should only contain one participant with a stoichiometry >= 2 or participant stoichiometry null and participant is not self/putative self.
static BinaryInteractionEvidence	InteractionUtils.createBinaryInteractionEvidenceFrom(InteractionEvidence interaction)	Create a BinaryInteractionEvidenceWrapper from the given interaction evidence which should contain not more than two participants
static ComplexType	InteractionUtils.findInteractionEvidenceCategoryOf(InteractionEvidence interaction)	The method will find the interactionCategory (binary, self, etc.)

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

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

Modifier and Type	Method	Description
static void	InteractionCloner.copyAndOverrideInteractionEvidenceProperties(InteractionEvidence source, InteractionEvidence target, boolean createNewParticipant, boolean ignoreParticipants)	This method will copy properties of interaction source in interaction target and will override all the other properties of Target interaction.
static void	InteractionCloner.copyAndOverrideParticipantsEvidencesToBinary(InteractionEvidence source, BinaryInteractionEvidence target, boolean createNewParticipant, boolean self)	This method will copy participants of interaction evidence source in binary target.

Uses of InteractionEvidence in psidev.psi.mi.jami.utils.comparator.interaction

Methods in psidev.psi.mi.jami.utils.comparator.interaction with parameters of type InteractionEvidence

Modifier and Type	Method	Description
static boolean	DefaultCuratedInteractionEvidenceComparator.areEquals(InteractionEvidence experimentalInteraction1, InteractionEvidence experimentalInteraction2)	Use DefaultCuratedInteractionEvidenceComparator to know if two experimental interactions are equals.
static boolean	DefaultExactCuratedInteractionEvidenceComparator.areEquals(InteractionEvidence experimentalInteraction1, InteractionEvidence experimentalInteraction2)	Use DefaultExactCuratedInteractionEvidenceComparator to know if two experimental interactions are equals.
static boolean	DefaultExactInteractionEvidenceComparator.areEquals(InteractionEvidence experimentalInteraction1, InteractionEvidence experimentalInteraction2)	Use DefaultExactInteractionEvidenceComparator to know if two experimental interactions are equals.
static boolean	DefaultInteractionEvidenceComparator.areEquals(InteractionEvidence experimentalInteraction1, InteractionEvidence experimentalInteraction2)	Use DefaultInteractionEvidenceComparator to know if two experimental interactions are equals.
static boolean	UnambiguousCuratedInteractionEvidenceComparator.areEquals(InteractionEvidence interaction1, InteractionEvidence interaction2)	Use UnambiguousCuratedInteractionEvidenceComparator to know if two experimental interactions are equals.
static boolean	UnambiguousExactCuratedInteractionEvidenceComparator.areEquals(InteractionEvidence interaction1, InteractionEvidence interaction2)	Use UnambiguousExactCuratedInteractionEvidenceComparator to know if two experimental interactions are equals.
static boolean	UnambiguousExactInteractionEvidenceComparator.areEquals(InteractionEvidence interaction1, InteractionEvidence interaction2)	Use UnambiguousExactInteractionEvidenceComparator to know if two experimental interactions are equals.
static boolean	UnambiguousInteractionEvidenceComparator.areEquals(InteractionEvidence interaction1, InteractionEvidence interaction2)	Use UnambiguousInteractionEvidenceComparator to know if two experimental interactions are equals.
int	InteractionEvidenceComparator.compare(InteractionEvidence experimentalInteraction1, InteractionEvidence experimentalInteraction2)	It will first compare the basic interaction properties using Comparator of type Interaction.
int	UnambiguousCuratedInteractionEvidenceComparator.compare(InteractionEvidence interaction1, InteractionEvidence interaction2)	It will first compare the basic interaction properties using UnambiguousCuratedInteractionBaseComparator.
int	UnambiguousExactCuratedInteractionEvidenceComparator.compare(InteractionEvidence interaction1, InteractionEvidence interaction2)	It will first compare the basic interaction properties using UnambiguousCuratedInteractionBaseComparator.
int	UnambiguousExactInteractionEvidenceComparator.compare(InteractionEvidence interaction1, InteractionEvidence interaction2)	It will first compare the basic interaction properties using UnambiguousInteractionBaseComparator.
int	UnambiguousInteractionEvidenceComparator.compare(InteractionEvidence interaction1, InteractionEvidence interaction2)	It will first compare the basic interaction properties using UnambiguousInteractionBaseComparator.

Uses of InteractionEvidence in psidev.psi.mi.jami.xml.io.iterator

Constructor parameters in psidev.psi.mi.jami.xml.io.iterator with type arguments of type InteractionEvidence

Constructor	Description
XmlInteractionEvidenceIterator(PsiXmlParser<InteractionEvidence> lineParser)	Constructor for XmlInteractionEvidenceIterator.

Uses of InteractionEvidence in psidev.psi.mi.jami.xml.io.parser

Methods in psidev.psi.mi.jami.xml.io.parser that return types with arguments of type InteractionEvidence

Modifier and Type	Method	Description
AbstractEntrySet<AbstractBaseEntry<InteractionEvidence>>	FullXmlBinaryEvidenceParser.getEntrySet()	getEntrySet.
protected ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>	FullXmlBinaryEvidenceParser.initialiseDefaultExpansionMethod()	initialiseDefaultExpansionMethod.
protected ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>	XmlBinaryEvidenceParser.initialiseDefaultExpansionMethod()	initialiseDefaultExpansionMethod.

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

Classes in psidev.psi.mi.jami.xml.io.writer.compact with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	AbstractCompactXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence>	Abstract class for a compact PSI-XML writer of mixed interactions

Methods in psidev.psi.mi.jami.xml.io.writer.compact with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected void	CompactXmlEvidenceWriter.registerAvailabilities(InteractionEvidence interaction)	registerAvailabilities.
protected void	CompactXmlNamedEvidenceWriter.registerAvailabilities(InteractionEvidence interaction)	registerAvailabilities.
protected void	CompactXmlEvidenceWriter.registerExperiment(InteractionEvidence interaction)	registerExperiment.
protected void	CompactXmlNamedEvidenceWriter.registerExperiment(InteractionEvidence interaction)	registerExperiment.

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

Methods in psidev.psi.mi.jami.xml.io.writer.compact.extended with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected void	CompactXmlEvidenceWriter.registerAvailabilities(InteractionEvidence interaction)	registerAvailabilities.
protected void	CompactXmlEvidenceWriter.registerExperiment(InteractionEvidence interaction)	registerExperiment.

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

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

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>	Abstract class for interaction evidence writers

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

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

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>	Abstract class for interaction evidence writers

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

Classes in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30 with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>	Abstract class for interaction evidence writers in PSI-MI XML 3.0

Uses of InteractionEvidence 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 with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.
protected void	XmlNamedInteractionEvidenceWriter.writeNames(InteractionEvidence object)	writeNames.

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

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

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.
protected void	XmlNamedInteractionEvidenceWriter.writeNames(InteractionEvidence object)	writeNames.

Uses of InteractionEvidence 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 with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.
protected void	XmlNamedInteractionEvidenceWriter.writeNames(InteractionEvidence object)	writeNames.

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

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

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.
protected void	XmlNamedInteractionEvidenceWriter.writeNames(InteractionEvidence object)	writeNames.

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

Classes in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>	Abstract class for interaction evidence writers that write expanded interactions (having modelled, intramolecular properties, list of experiments, list of interaction types, etc.)

Uses of InteractionEvidence 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 with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.

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

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

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.

Uses of InteractionEvidence 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 with parameters of type InteractionEvidence

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.

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

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

Modifier and Type	Method	Description
protected void	XmlInteractionEvidenceWriter.writeAvailability(InteractionEvidence object)	writeAvailability.
protected CvTerm	XmlInteractionEvidenceWriter.writeExperiments(InteractionEvidence object)	writeExperiments.

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

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

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>	Abstract class for interaction evidence writers that write expanded interactions (having modelled, intramolecular properties, list of experiments, list of interaction types, etc.)

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

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

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>	Abstract class for interaction evidence writers that write expanded interactions (having modelled, intramolecular properties, list of experiments, list of interaction types, etc.)

Uses of InteractionEvidence in psidev.psi.mi.jami.xml.io.writer.expanded

Classes in psidev.psi.mi.jami.xml.io.writer.expanded with type parameters of type InteractionEvidence

Modifier and Type	Class	Description
class	AbstractExpandedXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence>	Abstract class for an expanded PSI-XML writer of mixed interactions

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

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

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlInteractionEvidence	Extended interaction evidence for PSI-XML 2,5 standards

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

Classes in psidev.psi.mi.jami.xml.model.extension.binary that implement InteractionEvidence

Modifier and Type	Class	Description
class	AbstractXmlBinaryInteractionEvidence	Abstract class for Xml BinaryInteractionEvidence
class	XmlBinaryInteractionEvidenceWrapper	Xml implementation of BinaryInteractionWrapper with a source locator

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

Modifier and Type	Method	Description
Collection<InteractionEvidence>	XmlModelledBinaryInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlModelledBinaryInteractionWrapper.getInteractionEvidences()	Interaction evidences supporting this modelled interaction.

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

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

Modifier and Type	Class	Description
class	XmlBinaryInteractionEvidence	Xml implementation of BinaryInteractionEvidence

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

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

Modifier and Type	Class	Description
class	XmlBinaryInteractionEvidence	Xml implementation of BinaryInteractionEvidence

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

Classes in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that implement InteractionEvidence

Modifier and Type	Class	Description
class	XmlBinaryInteractionEvidence	Xml implementation of BinaryInteractionEvidence
class	XmlBinaryInteractionEvidenceWrapper	Xml implementation of BinaryInteractionWrapper with a source locator

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

Modifier and Type	Method	Description
Collection<InteractionEvidence>	XmlModelledBinaryInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlModelledBinaryInteractionWrapper.getInteractionEvidences()	Interaction evidences supporting this modelled interaction.

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

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

Modifier and Type	Method	Description
protected Iterator<InteractionEvidence>	XmlEvidenceStreamSource.createXmlIterator()	createXmlIterator.

Uses of InteractionEvidence in psidev.psi.mi.jami.xml.model.extension.factory.xml25

Methods in psidev.psi.mi.jami.xml.model.extension.factory.xml25 with parameters of type InteractionEvidence

Modifier and Type	Method	Description
BinaryInteractionEvidence	XmlBinaryInteractionFactory.createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)	Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidences
BinaryInteractionEvidence	XmlBinaryInteractionFactory.createBinaryInteractionEvidenceWrapperFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence that wraps the given interaction
BinaryInteractionEvidence	XmlBinaryInteractionFactory.createSelfBinaryInteractionEvidenceFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence representing a self interaction

Uses of InteractionEvidence in psidev.psi.mi.jami.xml.model.extension.factory.xml30

Methods in psidev.psi.mi.jami.xml.model.extension.factory.xml30 with parameters of type InteractionEvidence

Modifier and Type	Method	Description
BinaryInteractionEvidence	XmlBinaryInteractionFactory.createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)	Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidences
BinaryInteractionEvidence	XmlBinaryInteractionFactory.createBinaryInteractionEvidenceWrapperFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence that wraps the given interaction
BinaryInteractionEvidence	XmlBinaryInteractionFactory.createSelfBinaryInteractionEvidenceFrom(InteractionEvidence interaction)	Creates a BinaryInteractionEvidence representing a self interaction

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

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

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidence	Xml implementation of InteractionEvidence
class	DefaultXmlInteractionEvidence	Xml implementation of InteractionEvidence
class	XmlInteractionEvidence	Xml implementation of InteractionEvidence

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

Modifier and Type	Method	Description
Collection<InteractionEvidence>	AbstractXmlExperiment.getInteractionEvidences()	getInteractionEvidences.
Collection<InteractionEvidence>	AbstractXmlModelledInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlBasicInteractionComplexWrapper.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlInteractionEvidenceComplexWrapper.getInteractionEvidences()	Interaction evidences supporting this modelled interaction.
Collection<InteractionEvidence>	XmlModelledInteractionComplexWrapper.getInteractionEvidences()	getInteractionEvidences.

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

Modifier and Type	Method	Description
boolean	AbstractXmlExperiment.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	AbstractXmlExperiment.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

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

Modifier and Type	Method	Description
boolean	AbstractXmlExperiment.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	AbstractXmlExperiment.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

Constructor parameters in psidev.psi.mi.jami.xml.model.extension.xml253 with type arguments of type InteractionEvidence

Constructor	Description
XmlExperimentalParticipantPool(AbstractXmlParticipant<InteractionEvidence,FeatureEvidence> delegate)	Constructor for XmlExperimentalParticipantPool.

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

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

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidence	Xml implementation of InteractionEvidence
class	DefaultXmlInteractionEvidence	Xml implementation of InteractionEvidence
class	XmlInteractionEvidence	Xml implementation of InteractionEvidence

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

Modifier and Type	Method	Description
Collection<InteractionEvidence>	AbstractXmlExperiment.getInteractionEvidences()	getInteractionEvidences.
Collection<InteractionEvidence>	AbstractXmlModelledInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlBasicInteractionComplexWrapper.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlInteractionEvidenceComplexWrapper.getInteractionEvidences()	Interaction evidences supporting this modelled interaction.
Collection<InteractionEvidence>	XmlModelledInteractionComplexWrapper.getInteractionEvidences()	getInteractionEvidences.

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

Modifier and Type	Method	Description
boolean	AbstractXmlExperiment.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	AbstractXmlExperiment.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

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

Modifier and Type	Method	Description
boolean	AbstractXmlExperiment.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	AbstractXmlExperiment.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

Constructor parameters in psidev.psi.mi.jami.xml.model.extension.xml254 with type arguments of type InteractionEvidence

Constructor	Description
XmlExperimentalParticipantPool(AbstractXmlParticipant<InteractionEvidence,FeatureEvidence> delegate)	Constructor for XmlExperimentalParticipantPool.

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

Subinterfaces of InteractionEvidence in psidev.psi.mi.jami.xml.model.extension.xml300

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlInteractionEvidence	Extended interaction evidence for PSI-XML 2,5 standards

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

Modifier and Type	Class	Description
class	AbstractXmlInteractionEvidence	Xml implementation of InteractionEvidence
class	DefaultXmlInteractionEvidence	Xml implementation of InteractionEvidence
class	XmlInteractionEvidence	Xml implementation of InteractionEvidence

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

Modifier and Type	Method	Description
Collection<InteractionEvidence>	AbstractXmlExperiment.getInteractionEvidences()	getInteractionEvidences.
Collection<InteractionEvidence>	AbstractXmlModelledInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlBasicInteractionComplexWrapper.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlInteractionEvidenceComplexWrapper.getInteractionEvidences()	Interaction evidences supporting this modelled interaction.
Collection<InteractionEvidence>	XmlModelledInteraction.getInteractionEvidences()	Getter for the field interactionEvidences.
Collection<InteractionEvidence>	XmlModelledInteractionComplexWrapper.getInteractionEvidences()	getInteractionEvidences.

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

Modifier and Type	Method	Description
boolean	AbstractXmlExperiment.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	AbstractXmlExperiment.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

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

Modifier and Type	Method	Description
boolean	AbstractXmlExperiment.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	AbstractXmlExperiment.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

Constructor parameters in psidev.psi.mi.jami.xml.model.extension.xml300 with type arguments of type InteractionEvidence

Constructor	Description
XmlExperimentalParticipantPool(AbstractXmlParticipant<InteractionEvidence,FeatureEvidence> delegate)	Constructor for XmlExperimentalParticipantPool.

Uses of InteractionEvidence 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 InteractionEvidence

Modifier and Type	Method	Description
Collection<InteractionEvidence>	AbstractComplexRef.getInteractionEvidences()	getInteractionEvidences.
Collection<InteractionEvidence>	AbstractExperimentRef.getInteractionEvidences()	getInteractionEvidences.

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

Modifier and Type	Method	Description
boolean	AbstractExperimentRef.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	AbstractExperimentRef.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

Method parameters in psidev.psi.mi.jami.xml.model.reference.xml253 with type arguments of type InteractionEvidence

Modifier and Type	Method	Description
boolean	AbstractExperimentRef.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	AbstractExperimentRef.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

Uses of InteractionEvidence 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 InteractionEvidence

Modifier and Type	Method	Description
Collection<InteractionEvidence>	AbstractComplexRef.getInteractionEvidences()	getInteractionEvidences.
Collection<InteractionEvidence>	AbstractExperimentRef.getInteractionEvidences()	getInteractionEvidences.

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

Modifier and Type	Method	Description
boolean	AbstractExperimentRef.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	AbstractExperimentRef.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

Method parameters in psidev.psi.mi.jami.xml.model.reference.xml254 with type arguments of type InteractionEvidence

Modifier and Type	Method	Description
boolean	AbstractExperimentRef.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	AbstractExperimentRef.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

Uses of InteractionEvidence 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 InteractionEvidence

Modifier and Type	Method	Description
Collection<InteractionEvidence>	AbstractComplexRef.getInteractionEvidences()	getInteractionEvidences.
Collection<InteractionEvidence>	AbstractExperimentRef.getInteractionEvidences()	getInteractionEvidences.

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

Modifier and Type	Method	Description
boolean	AbstractExperimentRef.addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	AbstractExperimentRef.removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

Method parameters in psidev.psi.mi.jami.xml.model.reference.xml300 with type arguments of type InteractionEvidence

Modifier and Type	Method	Description
boolean	AbstractExperimentRef.addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	AbstractExperimentRef.removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

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

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

Modifier and Type	Method	Description
List<InteractionEvidence>	ExperimentalEntry.JAXBInteractionsWrapper.getJAXBInteractions()

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

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

Modifier and Type	Method	Description
List<InteractionEvidence>	ExperimentalEntry.JAXBInteractionsWrapper.getJAXBInteractions()

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

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

Modifier and Type	Method	Description
List<InteractionEvidence>	ExperimentalEntry.JAXBInteractionsWrapper.getJAXBInteractions()