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

Packages that use FeatureEvidence

Package	Description
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher.impl
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.html
psidev.psi.mi.jami.json.elements
psidev.psi.mi.jami.listener
psidev.psi.mi.jami.listener.impl
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.tab.io.iterator
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator.feature
psidev.psi.mi.jami.utils.comparator.participant
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.extended.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30
psidev.psi.mi.jami.xml.model.extension
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300

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

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

Modifier and Type	Class	Description
class	CsvFeatureEvidence	CrossLink CSV extension for FeatureEvidence

Uses of FeatureEvidence in psidev.psi.mi.jami.enricher.impl

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

Modifier and Type	Method	Description
EntityEnricher<ExperimentalEntity,FeatureEvidence>	CompositeEntityEnricher.getExperimentalEntityEnricher()	Getter for the field experimentalEntityEnricher.

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

Modifier and Type	Method	Description
void	CompositeEntityEnricher.setExperimentalEntityEnricher(EntityEnricher<ExperimentalEntity,FeatureEvidence> experimentalEntityEnricher)	Setter for the field experimentalEntityEnricher.
void	CompositeParticipantEvidenceEnricher.setFeatureEnricher(FeatureEnricher<FeatureEvidence> enricher)	setFeatureEnricher.

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

Constructor	Description
CompositeParticipantEvidenceEnricher(ParticipantEnricher<ParticipantEvidence,FeatureEvidence> entityBaseEnricher)	Constructor for CompositeParticipantEvidenceEnricher.

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

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

Modifier and Type	Method	Description
FeatureEnricher<FeatureEvidence>	FullParticipantEvidenceUpdater.getFeatureEnricher()	The current enricher used for features.
FeatureEnricherListener<FeatureEvidence>	FullFeatureEvidenceEnricher.getFeatureEnricherListener()	Retrieves the listener of feature changes.
FeatureEnricherListener<FeatureEvidence>	FullFeatureEvidenceUpdater.getFeatureEnricherListener()	Retrieves the listener of feature changes.

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

Modifier and Type	Method	Description
void	FullFeatureEvidenceEnricher.processMinimalUpdates(FeatureEvidence objectToEnrich, FeatureEvidence objectSource)	processMinimalUpdates.
void	FullFeatureEvidenceUpdater.processMinimalUpdates(FeatureEvidence objectToEnrich, FeatureEvidence objectSource)	processMinimalUpdates.
protected void	FullFeatureEvidenceEnricher.processOtherProperties(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processOtherProperties.
protected void	FullFeatureEvidenceUpdater.processOtherProperties(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processOtherProperties.
protected void	FullFeatureEvidenceEnricher.processParameters(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processParameters.
protected void	FullFeatureEvidenceUpdater.processParameters(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processParameters.

Method parameters in psidev.psi.mi.jami.enricher.impl.full with type arguments of type FeatureEvidence

Modifier and Type	Method	Description
void	FullParticipantEvidenceUpdater.setFeatureEnricher(FeatureEnricher<FeatureEvidence> featureEnricher)	setFeatureEnricher.
void	FullFeatureEvidenceEnricher.setFeatureEnricherListener(FeatureEnricherListener<FeatureEvidence> featureEnricherListener)	setFeatureEnricherListener.
void	FullFeatureEvidenceUpdater.setFeatureEnricherListener(FeatureEnricherListener<FeatureEvidence> featureEnricherListener)	setFeatureEnricherListener.

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

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

Modifier and Type	Method	Description
FeatureEnricher<FeatureEvidence>	MinimalParticipantEvidenceUpdater.getFeatureEnricher()	The current enricher used for features.
FeatureEnricherListener<FeatureEvidence>	MinimalFeatureEvidenceUpdater.getFeatureEnricherListener()	Retrieves the listener of feature changes.
protected MinimalFeatureUpdater<FeatureEvidence>	MinimalFeatureEvidenceUpdater.getMinimalUpdater()	Getter for the field minimalUpdater.
protected MinimalParticipantUpdater<P,FeatureEvidence>	MinimalParticipantEvidenceUpdater.getMinimalUpdater()	Getter for the field minimalUpdater.

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

Modifier and Type	Method	Description
protected void	MinimalFeatureEvidenceEnricher.mergeDetectionMethods(FeatureEvidence termToEnrich, Collection<CvTerm> toEnrichTerms, Collection<CvTerm> fetchedTerms, boolean remove)	Takes two lists of detection methods and produces a list of those to add and those to remove.
protected void	MinimalFeatureEvidenceUpdater.onInvalidRange(FeatureEvidence feature, Range range, Collection<String> errorMessages)	onInvalidRange.
protected void	MinimalFeatureEvidenceUpdater.onOutOfDateRange(FeatureEvidence feature, Range range, Collection<String> errorMessages, String oldSequence)	onOutOfDateRange.
protected void	MinimalFeatureEvidenceEnricher.processDetectionMethods(FeatureEvidence featureToEnrich)	processDetectionMethods.
protected void	MinimalFeatureEvidenceEnricher.processDetectionMethods(FeatureEvidence featureToEnrich, FeatureEvidence source)	processDetectionMethods.
protected void	MinimalFeatureEvidenceUpdater.processDetectionMethods(FeatureEvidence featureToEnrich, FeatureEvidence source)	processDetectionMethods.
protected void	MinimalFeatureEvidenceEnricher.processOtherProperties(FeatureEvidence featureToEnrich)	processOtherProperties.
protected void	MinimalFeatureEvidenceEnricher.processOtherProperties(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processOtherProperties.

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

Modifier and Type	Method	Description
void	MinimalParticipantEvidenceUpdater.setFeatureEnricher(FeatureEnricher<FeatureEvidence> featureEnricher)	setFeatureEnricher.
void	MinimalFeatureEvidenceUpdater.setFeatureEnricherListener(FeatureEnricherListener<FeatureEvidence> featureEnricherListener)	setFeatureEnricherListener.

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

Constructor	Description
MinimalFeatureEvidenceUpdater(MinimalFeatureUpdater<FeatureEvidence> minimalUpdater)	Constructor for MinimalFeatureEvidenceUpdater.
MinimalParticipantEvidenceUpdater(MinimalParticipantUpdater<P,FeatureEvidence> delegate)	Constructor for MinimalParticipantEvidenceUpdater.

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

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

Modifier and Type	Method	Description
void	FeatureEvidenceEnricherListenerManager.onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)	onAddedDetectionMethod
void	FeatureEvidenceEnricherListenerManager.onAddedParameter(FeatureEvidence o, Parameter added)	Listen to the event where a parameter has been added to the object parameters.
void	FeatureEvidenceEnricherListenerManager.onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)	onRemovedDetectionMethod
void	FeatureEvidenceEnricherListenerManager.onRemovedParameter(FeatureEvidence o, Parameter removed)	Listen to the event where a parameter has been removed from the object parameters.

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

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

Modifier and Type	Method	Description
void	FeatureEvidenceEnricherLogger.onEnrichmentComplete(FeatureEvidence feature, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	FeatureEvidenceEnricherLogger.onEnrichmentError(FeatureEvidence object, String message, Exception e)	onEnrichmentError.

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

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

Modifier and Type	Method	Description
void	FeatureEvidenceEnricherStatisticsWriter.onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)	onAddedDetectionMethod
void	FeatureEvidenceEnricherStatisticsWriter.onAddedParameter(FeatureEvidence o, Parameter added)	Listen to the event where a parameter has been added to the object parameters.
void	FeatureEvidenceEnricherStatisticsWriter.onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)	onRemovedDetectionMethod
void	FeatureEvidenceEnricherStatisticsWriter.onRemovedParameter(FeatureEvidence o, Parameter removed)	Listen to the event where a parameter has been removed from the object parameters.

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

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

Modifier and Type	Method	Description
protected void	MIEvidenceHtmlWriter.writeDetectionMethods(FeatureEvidence feature)	writeDetectionMethods

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

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

Modifier and Type	Method	Description
protected void	SimpleJsonFeatureEvidenceWriter.writeOtherProperties(FeatureEvidence object)	writeOtherProperties.

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

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

Modifier and Type	Method	Description
void	FeatureEvidenceChangeListener.onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)	onAddedDetectionMethod
void	FeatureEvidenceChangeListener.onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)	onRemovedDetectionMethod

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

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

Modifier and Type	Method	Description
void	FeatureEvidenceChangeLogger.onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)	onAddedDetectionMethod
void	FeatureEvidenceChangeLogger.onAddedParameter(FeatureEvidence feature, Parameter added)	Listen to the event where a parameter has been added to the object parameters.
void	FeatureEvidenceChangeLogger.onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)	onRemovedDetectionMethod
void	FeatureEvidenceChangeLogger.onRemovedParameter(FeatureEvidence feature, Parameter removed)	Listen to the event where a parameter has been removed from the object parameters.

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

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

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

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

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

Modifier and Type	Class	Description
class	MitabFeatureEvidence	Mitab extension for FeatureEvidence

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

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

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

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

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

Modifier and Type	Method	Description
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, Collection<CvTerm> detectionMethods, Collection<Range> ranges)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, Collection<CvTerm> detectionMethods, Range range)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, Collection<Range> ranges)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, CvTerm detectionMethod, Collection<Range> ranges)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, CvTerm detectionMethod, Range range)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, Range range)	createFeatureEvidence

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

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

Modifier and Type	Method	Description
static void	FeatureCloner.copyAndOverrideFeatureEvidenceProperties(FeatureEvidence source, FeatureEvidence target)	This method will copy properties of Feature source in Feature target and will override all the other properties of Target feature.

Uses of FeatureEvidence in psidev.psi.mi.jami.utils.comparator.feature

Methods in psidev.psi.mi.jami.utils.comparator.feature with parameters of type FeatureEvidence

Modifier and Type	Method	Description
static boolean	DefaultFeatureEvidenceComparator.areEquals(FeatureEvidence experimentalFeature1, FeatureEvidence experimentalFeature2)	Use DefaultFeatureEvidenceComparator to know if two experimental features are equals.
static boolean	UnambiguousFeatureEvidenceComparator.areEquals(FeatureEvidence feature1, FeatureEvidence feature2)	Use UnambiguousFeatureEvidenceComparator to know if two experimental features are equals.
int	FeatureEvidenceComparator.compare(FeatureEvidence experimentalFeature1, FeatureEvidence experimentalFeature2)	It will first use a AbstractFeatureBaseComparator to compare basic properties of a feature.
int	UnambiguousFeatureEvidenceComparator.compare(FeatureEvidence experimentalFeature1, FeatureEvidence experimentalFeature2)	It will first compare feature detection methods using UnambiguousCvTermComparator.

Uses of FeatureEvidence in psidev.psi.mi.jami.utils.comparator.participant

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

Modifier and Type	Method	Description
CollectionComparator<FeatureEvidence>	ExperimentalEntityComparator.getFeatureCollectionComparator()	Getter for the field featureCollectionComparator.
CollectionComparator<FeatureEvidence>	ExperimentalParticipantPoolComparator.getFeatureCollectionComparator()	Getter for the field featureCollectionComparator.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.participant with type arguments of type FeatureEvidence

Constructor	Description
ExperimentalEntityComparator(EntityBaseComparator participantBaseComparator, CollectionComparator<FeatureEvidence> featuresComparator)	Creates a new ParticipantEvidenceComparator

Uses of FeatureEvidence 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 with parameters of type FeatureEvidence

Modifier and Type	Method	Description
protected void	AbstractXmlFeatureEvidenceWriter.writeFeatureDetectionMethod(FeatureEvidence object)	writeFeatureDetectionMethod.
protected void	AbstractXmlFeatureEvidenceWriter.writeOtherProperties(FeatureEvidence object)	writeOtherProperties.
protected void	AbstractXmlFeatureEvidenceWriter.writeParameters(FeatureEvidence object)	writeParameters.

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

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

Modifier and Type	Method	Description
protected void	AbstractXmlFeatureEvidenceWriter.writeFeatureDetectionMethod(FeatureEvidence object)	writeFeatureDetectionMethod.
protected void	AbstractXmlFeatureEvidenceWriter.writeOtherProperties(FeatureEvidence object)	writeOtherProperties.
protected void	AbstractXmlFeatureEvidenceWriter.writeParameters(FeatureEvidence object)	writeParameters.

Uses of FeatureEvidence 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 with parameters of type FeatureEvidence

Modifier and Type	Method	Description
protected void	XmlFeatureEvidenceWriter.writeOtherProperties(FeatureEvidence object)	writeOtherProperties.

Uses of FeatureEvidence 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 with parameters of type FeatureEvidence

Modifier and Type	Method	Description
protected void	XmlFeatureEvidenceWriter.writeOtherProperties(FeatureEvidence object)	writeOtherProperties.

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

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

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlFeatureEvidence	PSI-XML extension of a feature evidence

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

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

Modifier and Type	Class	Description
class	XmlFeatureEvidence	Xml implementation of a Feature

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

Modifier and Type	Method	Description
List<FeatureEvidence>	XmlExperimentalParticipantCandidate.JAXBFeatureWrapper.getJAXBFeatures()
List<FeatureEvidence>	XmlParticipantEvidence.JAXBFeatureWrapper.getJAXBFeatures()

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

Modifier and Type	Method	Description
void	XmlExperimentalParticipantCandidate.processAddedFeature(FeatureEvidence feature)	processAddedFeature.
void	XmlParticipantEvidence.processAddedFeature(FeatureEvidence feature)	processAddedFeature.

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

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

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

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

Modifier and Type	Class	Description
class	XmlFeatureEvidence	Xml implementation of a Feature

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

Modifier and Type	Method	Description
List<FeatureEvidence>	XmlExperimentalParticipantCandidate.JAXBFeatureWrapper.getJAXBFeatures()
List<FeatureEvidence>	XmlParticipantEvidence.JAXBFeatureWrapper.getJAXBFeatures()

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

Modifier and Type	Method	Description
void	XmlExperimentalParticipantCandidate.processAddedFeature(FeatureEvidence feature)	processAddedFeature.
void	XmlParticipantEvidence.processAddedFeature(FeatureEvidence feature)	processAddedFeature.

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

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

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

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

Modifier and Type	Class	Description
class	XmlFeatureEvidence	Xml implementation of a Feature

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

Modifier and Type	Method	Description
List<FeatureEvidence>	XmlExperimentalParticipantCandidate.JAXBFeatureWrapper.getJAXBFeatures()
List<FeatureEvidence>	XmlParticipantEvidence.JAXBFeatureWrapper.getJAXBFeatures()

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

Modifier and Type	Method	Description
void	XmlExperimentalParticipantCandidate.processAddedFeature(FeatureEvidence feature)	processAddedFeature.
void	XmlParticipantEvidence.processAddedFeature(FeatureEvidence feature)	processAddedFeature.

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

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