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

Packages that use Feature

Package	Description
psidev.psi.mi.jami.analysis.graph
psidev.psi.mi.jami.analysis.graph.model
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher
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
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.enricher.util
psidev.psi.mi.jami.html
psidev.psi.mi.jami.json.binary.elements
psidev.psi.mi.jami.json.elements
psidev.psi.mi.jami.json.nary
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.feeder
psidev.psi.mi.jami.tab.io.writer.feeder.extended
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator.feature
psidev.psi.mi.jami.xml
psidev.psi.mi.jami.xml.cache
psidev.psi.mi.jami.xml.io.writer.elements
psidev.psi.mi.jami.xml.io.writer.elements.impl
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30
psidev.psi.mi.jami.xml.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
psidev.psi.mi.jami.xml.model.reference
psidev.psi.mi.jami.xml.model.reference.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300

Uses of Feature in psidev.psi.mi.jami.analysis.graph

Classes in psidev.psi.mi.jami.analysis.graph with type parameters of type Feature

Modifier and Type	Class	Description
class	BindingPairFactory<F extends Feature>	A feature edge factory is an edge factory generating FeatureBindingPairs The factory can be instantiated with a specific MIComparator if it wants to override the comparison and hashcodes of features A and B
class	BindingSiteCliqueFinder<I extends Interaction,F extends Feature>	The BindingSiteClique finder is an extension of BronKerboschCliqueFinder.
class	FeatureGraphBuilder<I extends Interaction,F extends Feature>	This class will create a graph from one to several interactions.

Uses of Feature in psidev.psi.mi.jami.analysis.graph.model

Classes in psidev.psi.mi.jami.analysis.graph.model with type parameters of type Feature

Modifier and Type	Class	Description
class	BindingFeatureGraph<T extends Feature>	A binding feature graph is a pseudograph of binding features.
class	BindingPair<F extends Feature>	A feature binding pair is an undirected MI edge of features that are linked to each other.

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

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

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

Uses of Feature in psidev.psi.mi.jami.enricher

Classes in psidev.psi.mi.jami.enricher with type parameters of type Feature

Modifier and Type	Interface	Description
interface	EntityEnricher<P extends Entity,F extends Feature>	Sub enrichers: Protein, CvTerm, Feature, Bioactive3Entity
interface	FeatureEnricher<F extends Feature>	The featureEnricher can enrich either a single feature or a collection.
interface	ParticipantEnricher<P extends Participant,F extends Feature>	Sub enrichers: Protein, CvTerm, Feature, Bioactive3Entity
interface	ParticipantPoolEnricher<P extends ParticipantPool,F extends Feature>	Sub enrichers: Protein, CvTerm, Feature, Bioactive3Entity
interface	ProteinListeningFeatureEnricher<F extends Feature>	An extension to the feature enricher, the protein listening form also updates ranges.

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

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

Modifier and Type	Method	Description
EntityEnricher<Entity,Feature>	CompositeEntityEnricher.getEntityBaseEnricher()	Getter for the field entityBaseEnricher.
ParticipantEnricher<Participant,Feature>	CompositeParticipantEnricher.getEntityBaseEnricher()	Getter for the field entityBaseEnricher.
ParticipantPoolEnricher<ParticipantPool,Feature>	CompositeParticipantEnricher.getPoolEnricher()	Getter for the field poolEnricher.

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

Modifier and Type	Method	Description
void	CompositeEntityEnricher.setFeatureEnricher(FeatureEnricher<Feature> enricher)	setFeatureEnricher.
void	CompositeParticipantEnricher.setFeatureEnricher(FeatureEnricher<Feature> enricher)	setFeatureEnricher.
void	CompositeParticipantEnricher.setPoolEnricher(ParticipantPoolEnricher<ParticipantPool,Feature> poolEnricher)	Setter for the field poolEnricher.

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

Constructor	Description
CompositeEntityEnricher(EntityEnricher<Entity,Feature> entityBaseEnricher)	Constructor for CompositeEntityEnricher.
CompositeParticipantEnricher(ParticipantEnricher<Participant,Feature> entityBaseEnricher)	Constructor for CompositeParticipantEnricher.

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

Classes in psidev.psi.mi.jami.enricher.impl.full with type parameters of type Feature

Modifier and Type	Class	Description
class	FullEntityEnricher<P extends Entity,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.
class	FullEntityUpdater<P extends Entity,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.
class	FullFeatureEnricher<F extends Feature>	Provides full enrichment of feature.
class	FullFeatureUpdater<F extends Feature>	Provides full updater of feature.
class	FullParticipantEnricher<P extends Participant,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.
class	FullParticipantPoolEnricher<P extends ParticipantPool,F extends Feature>	The participant pool enricher is an enricher which can enrich either single participant or a collection.
class	FullParticipantPoolUpdater<P extends ParticipantPool,F extends Feature>	The participant pool enricher is an enricher which can enrich either single participant or a collection.
class	FullParticipantUpdater<P extends Participant,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.

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

Classes in psidev.psi.mi.jami.enricher.impl.minimal with type parameters of type Feature

Modifier and Type	Class	Description
class	MinimalEntityEnricher<P extends Entity,F extends Feature>	The entity enricher is an enricher which can enrich either single participant or a collection.
class	MinimalEntityUpdater<P extends Entity,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.
class	MinimalFeatureEnricher<F extends Feature>	Provides minimal enrichment of feature.
class	MinimalFeatureUpdater<F extends Feature>	Provides minimal update of feature.
class	MinimalParticipantEnricher<P extends Participant,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.
class	MinimalParticipantPoolEnricher<P extends ParticipantPool,F extends Feature>	The participant pool enricher is an enricher which can enrich either single participant or a collection.
class	MinimalParticipantPoolUpdater<P extends ParticipantPool,F extends Feature>	The participant pool enricher is an enricher which can enrich either single participant or a collection.
class	MinimalParticipantUpdater<P extends Participant,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.

Uses of Feature in psidev.psi.mi.jami.enricher.listener

Classes in psidev.psi.mi.jami.enricher.listener with type parameters of type Feature

Modifier and Type	Interface	Description
interface	FeatureEnricherListener<T extends Feature>	An extension of the FeatureChangeListener with specific methods related to the process of enriching.

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

Classes in psidev.psi.mi.jami.enricher.listener.impl with type parameters of type Feature

Modifier and Type	Class	Description
class	FeatureEnricherListenerManager<T extends Feature>	A manager for listeners which holds a list of listeners.

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

Modifier and Type	Method	Description
void	EntityEnricherListenerManager.onAddedFeature(P participant, Feature added)	onAddedFeature
void	EntityEnricherListenerManager.onRemovedFeature(P participant, Feature removed)	onRemovedFeature

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

Classes in psidev.psi.mi.jami.enricher.listener.impl.log with type parameters of type Feature

Modifier and Type	Class	Description
class	FeatureEnricherLogger<T extends Feature>	A logging listener.

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

Classes in psidev.psi.mi.jami.enricher.listener.impl.writer with type parameters of type Feature

Modifier and Type	Class	Description
class	FeatureEnricherStatisticsWriter<T extends Feature>	A statistics logger which records changes made by the enricher.

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

Modifier and Type	Method	Description
void	EntityEnricherStatisticsWriter.onAddedFeature(P participant, Feature added)	onAddedFeature
void	EntityEnricherStatisticsWriter.onRemovedFeature(P participant, Feature removed)	onRemovedFeature

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

Methods in psidev.psi.mi.jami.enricher.util with type parameters of type Feature

Modifier and Type	Method	Description
static <F extends Feature> void	EnricherUtils.mergeFeatures(Entity termToEnrich, Collection<F> toEnrichFeatures, Collection<F> fetchedFeatures, boolean remove, EntityChangeListener entityListener, FeatureEnricher<F> featureEnricher)	mergeFeatures.
static <T extends Feature> void	EnricherUtils.mergeRanges(T termToEnrich, Collection<Range> toEnrichRanges, Collection<Range> fetchedRanges, boolean remove, FeatureChangeListener<T> featureListener)	mergeRanges.

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

Classes in psidev.psi.mi.jami.html with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractMIHtmlWriter<T extends Interaction,P extends Participant,F extends Feature>	Abstract class for MI HTML writer

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

Modifier and Type	Method	Description
protected void	LightMIHtmlWriter.writeDetectionMethods(Feature feature)	writeDetectionMethods
protected void	MIHtmlWriter.writeDetectionMethods(Feature feature)	writeDetectionMethods

Uses of Feature in psidev.psi.mi.jami.json.binary.elements

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

Constructor	Description
SimpleJsonBinaryInteractionEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonBinaryInteractionEvidenceWriter.
SimpleJsonBinaryInteractionEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for SimpleJsonBinaryInteractionEvidenceWriter.
SimpleJsonBinaryInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonBinaryInteractionWriter.
SimpleJsonBinaryInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for SimpleJsonBinaryInteractionWriter.
SimpleJsonModelledBinaryInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonModelledBinaryInteractionWriter.
SimpleJsonModelledBinaryInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for SimpleJsonModelledBinaryInteractionWriter.

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

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

Modifier and Type	Class	Description
class	SimpleJsonFeatureWriter<F extends Feature>	Json writer for features

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

Modifier and Type	Method	Description
protected <F extends Feature> void	SimpleJsonParticipantWriter.writeAllFeatures(Collection<F> features)	writeAllFeatures.
protected <F extends Feature> void	SimpleJsonParticipantWriter.writeFeatures(String name, Collection<F> features)	writeFeatures.

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

Modifier and Type	Method	Description
protected Map<Feature,Integer>	SimpleJsonInteractionWriter.getProcessedFeatures()	Getter for the field processedFeatures.
protected Map<Feature,Integer>	SimpleJsonParticipantWriter.getProcessedFeatures()	Getter for the field processedFeatures.

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

Modifier and Type	Method	Description
void	JsonRangeWriter.write(Range object, Feature parent)	write.
void	SimpleJsonRangeWriter.write(Range object, Feature parent)	write.

Constructor parameters in psidev.psi.mi.jami.json.elements with type arguments of type Feature

Constructor	Description
SimpleJsonFeatureEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonFeatureEvidenceWriter.
SimpleJsonFeatureEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator, OntologyTermFetcher fetcher)	Constructor for SimpleJsonFeatureEvidenceWriter.
SimpleJsonFeatureWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonFeatureWriter.
SimpleJsonFeatureWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator, OntologyTermFetcher fetcher)	Constructor for SimpleJsonFeatureWriter.
SimpleJsonInteractionEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonInteractionEvidenceWriter.
SimpleJsonInteractionEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for SimpleJsonInteractionEvidenceWriter.
SimpleJsonInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonInteractionWriter.
SimpleJsonInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for SimpleJsonInteractionWriter.
SimpleJsonModelledFeatureWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonModelledFeatureWriter.
SimpleJsonModelledFeatureWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator, OntologyTermFetcher fetcher)	Constructor for SimpleJsonModelledFeatureWriter.
SimpleJsonModelledInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonModelledInteractionWriter.
SimpleJsonModelledInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for SimpleJsonModelledInteractionWriter.
SimpleJsonModelledParticipantWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonModelledParticipantWriter.
SimpleJsonModelledParticipantWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator, OntologyTermFetcher fetcher)	Constructor for SimpleJsonModelledParticipantWriter.
SimpleJsonParticipantEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonParticipantEvidenceWriter.
SimpleJsonParticipantEvidenceWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator, OntologyTermFetcher fetcher)	Constructor for SimpleJsonParticipantEvidenceWriter.
SimpleJsonParticipantWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonParticipantWriter.
SimpleJsonParticipantWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator, OntologyTermFetcher fetcher)	Constructor for SimpleJsonParticipantWriter.

Uses of Feature in psidev.psi.mi.jami.json.nary

Methods in psidev.psi.mi.jami.json.nary that return types with arguments of type Feature

Modifier and Type	Method	Description
protected Map<Feature,Integer>	AbstractMIJsonWriter.getProcessedFeatures()	Getter for the field processedFeatures.

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

Classes in psidev.psi.mi.jami.listener with type parameters of type Feature

Modifier and Type	Interface	Description
interface	FeatureChangeListener<F extends Feature>	Listener to feature change events

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

Modifier and Type	Method	Description
void	EntityChangeListener.onAddedFeature(F participant, Feature added)	onAddedFeature
void	EntityChangeListener.onRemovedFeature(F participant, Feature removed)	onRemovedFeature

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

Classes in psidev.psi.mi.jami.listener.impl with type parameters of type Feature

Modifier and Type	Class	Description
class	FeatureChangeLogger<T extends Feature>	This listener will just interactor change events

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

Modifier and Type	Method	Description
void	EntityChangeLogger.onAddedFeature(T entity, Feature added)	onAddedFeature
void	ParticipantChangeLogger.onAddedFeature(T entity, Feature added)	onAddedFeature
void	EntityChangeLogger.onRemovedFeature(T entity, Feature removed)	onRemovedFeature
void	ParticipantChangeLogger.onRemovedFeature(T entity, Feature removed)	onRemovedFeature

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

Classes in psidev.psi.mi.jami.model with type parameters of type Feature

Modifier and Type	Interface	Description
interface	Entity<F extends Feature>	An entity which gives more information to a specific molecule (such as features, causal relationships)
interface	Feature<P extends Entity,F extends Feature>	Property of a participant that may interfere with the binding of a molecule.
interface	NamedParticipant<I extends Interaction,F extends Feature>	A named entity is an entity having a short name and a fullname in addition to aliases.
interface	Participant<I extends Interaction,F extends Feature>	Participant identified in an interaction
interface	ParticipantCandidate<P extends ParticipantPool,F extends Feature>	A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationships
interface	ParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	A pool of participants that can be grouped together as a single participant as they are interchangeable

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

Modifier and Type	Interface	Description
interface	FeatureEvidence	The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
interface	ModelledFeature	Biological property of a participant that may be involved with or interfere with the binding of a molecule.

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

Classes in psidev.psi.mi.jami.model.impl with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractEntity<F extends Feature>	Abstract class for Entity
class	AbstractFeature<P extends Entity,F extends Feature>	Abstract class for Feature
class	AbstractParticipant<I extends Interaction,F extends Feature>	Abstract class for Participant
class	AbstractParticipantCandidate<P extends ParticipantPool,F extends Feature>	Abstract class for participant candidate
class	AbstractParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for Participant pool

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

Modifier and Type	Class	Description
class	AbstractFeature<P extends Entity,F extends Feature>	Abstract class for Feature
class	DefaultFeature	Default implementation for feature Notes: The equals and hashcode methods have NOT been overridden because the Feature object is a complex object.
class	DefaultFeatureEvidence	Default implementation for FeatureEvidence Notes: The equals and hashcode methods have NOT been overridden because the FeatureEvidence object is a complex object.
class	DefaultModelledFeature	Default implementation for ModelledFeature Notes: The equals and hashcode methods have NOT been overridden because the ModelledFeature object is a complex object.

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

Classes in psidev.psi.mi.jami.tab.extension with type parameters of type Feature

Modifier and Type	Interface	Description
interface	MitabFeature<P extends Entity,F extends Feature>	Basic interface for Mitab features

Subinterfaces of Feature in psidev.psi.mi.jami.tab.extension

Modifier and Type	Interface	Description
interface	MitabFeature<P extends Entity,F extends Feature>	Basic interface for Mitab features

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

Modifier and Type	Class	Description
class	DefaultMitabFeature	A DefaultMitabFeature is a feature in MITAB with some free text.
class	MitabFeatureEvidence	Mitab extension for FeatureEvidence
class	MitabModelledFeature	Mitab extension of ModelledFeature

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

Classes in psidev.psi.mi.jami.tab.extension.datasource with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractMitabSource<T extends Interaction,P extends Participant,F extends Feature>	Abstract class for an InteractionSource coming from a MITAB file.
class	AbstractMitabStreamSource<T extends Interaction,P extends Participant,F extends Feature>	abstract class for Mitab datasource.

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

Classes in psidev.psi.mi.jami.tab.io.iterator with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractMitabIterator<T extends Interaction,P extends Participant,F extends Feature>	Abstract class for mitab iterator

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

Constructor	Description
MitabBinaryIterator(MitabLineParser<BinaryInteraction,Participant,Feature> lineParser)	Constructor for MitabBinaryIterator.
MitabInteractionIterator(MitabLineParser<Interaction,Participant,Feature> lineParser)	Constructor for MitabInteractionIterator.

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

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

Modifier and Type	Class	Description
class	AbstractInteractionLineParser<T extends Interaction,P extends Participant,F extends Feature>	Abstract mitab line parser
class	MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

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

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

Modifier and Type	Method	Description
void	AbstractMitabColumnFeeder.writeFeature(Feature feature)	Writes a feature
void	MitabColumnFeeder.writeFeature(Feature feature)	Writes a feature

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

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

Modifier and Type	Method	Description
void	DefaultExtendedMitabColumnFeeder.writeFeature(Feature feature)	Writes a feature
void	ExtendedMitabInteractionEvidenceFeeder.writeFeature(Feature feature)	Writes a feature
void	ExtendedMitabModelledInteractionFeeder.writeFeature(Feature feature)	Writes a feature

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

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

Modifier and Type	Method	Description
static Feature	FeatureUtils.createDefaultFeature(String name, CvTerm featureType, Collection<Range> ranges)	createDefaultFeature
static Feature	FeatureUtils.createDefaultFeature(String name, CvTerm featureType, Range range)	createDefaultFeature

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

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

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

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

Classes in psidev.psi.mi.jami.utils.comparator.feature with type parameters of type Feature

Modifier and Type	Class	Description
class	FeatureCollectionComparator<T extends Feature>	Comparator for collection of Features

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

Modifier and Type	Method	Description
Comparator<Feature>	FeatureComparator.getFeatureBaseComparator()	Getter for the field featureBaseComparator.
Comparator<Feature>	FeatureEvidenceComparator.getFeatureComparator()	Getter for the field featureComparator.
Comparator<Feature>	ModelledFeatureComparator.getFeatureComparator()	Getter for the field featureComparator.

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

Modifier and Type	Method	Description
static boolean	DefaultFeatureBaseComparator.areEquals(Feature feature1, Feature feature2)	Use DefaultFeatureBaseComparator to know if two features are equals.
static boolean	DefaultFeatureComparator.areEquals(Feature feature1, Feature feature2)	Use DefaultFeatureComparator to know if two features are equals.
static boolean	UnambiguousFeatureBaseComparator.areEquals(Feature feature1, Feature feature2)	Use UnambiguousFeatureBaseComparator to know if two features are equals.
static boolean	UnambiguousFeatureComparator.areEquals(Feature feature1, Feature feature2)	Use UnambiguousFeatureComparator to know if two features are equals.
int	FeatureBaseComparator.compare(Feature feature1, Feature feature2)	It will look first at the feature shortnames (case insensitive).
int	FeatureComparator.compare(Feature feature1, Feature feature2)	Biological features come first and then experimental features.
int	UnambiguousFeatureComparator.compare(Feature feature1, Feature feature2)	Biological features come first and then experimental features.
static int	UnambiguousFeatureBaseComparator.hashCode(Feature feature)	hashCode

Constructor parameters in psidev.psi.mi.jami.utils.comparator.feature with type arguments of type Feature

Constructor	Description
FeatureComparator(Comparator<Feature> featureBaseComparator, Comparator<CvTerm> cvTermComparator)	Constructor for FeatureComparator.
FeatureEvidenceComparator(Comparator<Feature> featureComparator, Comparator<CvTerm> cvTermComparator)	Creates a new FeatureEvidenceComparator.
FeatureEvidenceComparator(Comparator<Feature> featureComparator, CollectionComparator<CvTerm> cvTermComparator)	Constructor for FeatureEvidenceComparator.
ModelledFeatureComparator(Comparator<Feature> featureComparator)	Creates a new ModelledFeatureComparator.

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

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

Modifier and Type	Method	Description
void	XmlEntryContext.registerFeature(int id, Feature o)	registerFeature.

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

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

Modifier and Type	Method	Description
Feature	InMemoryPsiXmlCache.getFeature(int id)	getFeature.
Feature	PsiXmlFileIndexCache.getFeature(int id)	getFeature.
Feature	PsiXmlIdCache.getFeature(int id)	getFeature.

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

Modifier and Type	Method	Description
int	InMemoryIdentityObjectCache.extractIdForFeature(Feature o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
int	InMemoryLightIdentityObjectCache.extractIdForFeature(Feature o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
int	PsiXmlObjectCache.extractIdForFeature(Feature o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
void	InMemoryPsiXmlCache.registerFeature(int id, Feature object)	Register a feature with an id
void	PsiXmlFileIndexCache.registerFeature(int id, Feature object)	Register a feature with an id
void	PsiXmlIdCache.registerFeature(int id, Feature object)	Register a feature with an id
ModelledFeature	InMemoryPsiXmlCache.registerModelledFeatureLoadedFrom(Feature f)	registerModelledFeatureLoadedFrom.
ModelledFeature	PsiXmlFileIndexCache.registerModelledFeatureLoadedFrom(Feature f)	registerModelledFeatureLoadedFrom.
ModelledFeature	PsiXmlIdCache.registerModelledFeatureLoadedFrom(Feature f)	registerModelledFeatureLoadedFrom.

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

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

Modifier and Type	Method	Description
static <F extends Feature> PsiXmlElementWriter<F>[]	PsiXmlElementWriterFactory.createFeatureWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, InteractionCategory category, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVariableNameWriter<CvTerm> featureTypeWriter, PsiXmlParameterWriter parameterWriter)	createFeatureWriter.

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

Modifier and Type	Method	Description
static PsiXmlElementWriter<Set<Feature>>	PsiXmlElementWriterFactory.createBindingFeaturesWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createBindingFeaturesWriter.
static PsiXmlElementWriter<Set<Feature>>	PsiXmlElementWriterFactory.createInferredInteractionWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createInferredInteractionWriter.

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

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

Modifier and Type	Method	Description
void	XmlInferredInteractionWriter.write(Set<Feature> object)	write.

Uses of Feature 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 Feature

Modifier and Type	Class	Description
class	AbstractXmlFeatureWriter<F extends Feature>	Abstract writer for Xml25Feature.
class	AbstractXmlParticipantWriter<P extends Participant,F extends Feature>	Abstract Xml writer for participant

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

Modifier and Type	Method	Description
protected Collection<Set<Feature>>	AbstractXmlInteractionWriter.collectInferredInteractionsFrom(T object)	collectInferredInteractionsFrom.
PsiXmlElementWriter<Set<Feature>>	AbstractXmlInteractionWriter.getInferredInteractionWriter()	Getter for the field inferredInteractionWriter.

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

Modifier and Type	Method	Description
void	AbstractXmlInteractionWriter.setInferredInteractionWriter(PsiXmlElementWriter<Set<Feature>> inferredInteractionWriter)	Setter for the field inferredInteractionWriter.

Uses of Feature 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 Feature

Modifier and Type	Class	Description
class	AbstractXmlFeatureWriter<F extends Feature>	Abstract writer for Xml25Feature.

Uses of Feature 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 Feature

Modifier and Type	Class	Description
class	AbstractXmlFeatureWriter<F extends Feature>	Abstract writer for Xml30Feature.
class	AbstractXmlParticipantCandidateWriter<P extends ParticipantCandidate,F extends Feature>	Abstract Xml writer for participant candidate

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

Modifier and Type	Method	Description
PsiXmlElementWriter<Set<Feature>>	AbstractXmlModelledInteractionWriter.getBindingFeaturesWriter()	Getter for the field bindingFeaturesWriter.

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

Modifier and Type	Method	Description
void	AbstractXmlModelledInteractionWriter.setBindingFeaturesWriter(PsiXmlElementWriter<Set<Feature>> bindingFeaturesWriter)	Setter for the field bindingFeaturesWriter.

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

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

Modifier and Type	Method	Description
PsiXmlElementWriter<Set<Feature>>	AbstractXmlModelledInteractionWriter.getBindingFeaturesWriter()	Getter for the field bindingFeaturesWriter.

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

Modifier and Type	Method	Description
void	AbstractXmlModelledInteractionWriter.setBindingFeaturesWriter(PsiXmlElementWriter<Set<Feature>> bindingFeaturesWriter)	Setter for the field bindingFeaturesWriter.

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

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

Modifier and Type	Method	Description
protected void	XmlFeatureWriter.writeOtherProperties(Feature object)	writeOtherProperties.

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

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

Modifier and Type	Method	Description
void	XmlBindingFeaturesWriter.write(Set<Feature> object)	write.

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

Classes in psidev.psi.mi.jami.xml.model.extension with type parameters of type Feature

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlEntity<F extends Feature>	Extended participant for PSI-XML 2,5 standards
interface	ExtendedPsiXmlFeature<P extends Entity,F extends Feature>	Interface for psi25 xml features
interface	ExtendedPsiXmlParticipant<I extends Interaction,F extends Feature>	Extended participant for PSI-XML 2,5 standards

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

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlFeature<P extends Entity,F extends Feature>	Interface for psi25 xml features
interface	ExtendedPsiXmlFeatureEvidence	PSI-XML extension of a feature evidence

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

Modifier and Type	Method	Description
Feature	AbstractInferredInteractionParticipant.getFeature()	Getter for the field feature.

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

Modifier and Type	Method	Description
void	AbstractInferredInteractionParticipant.setFeature(Feature feature)	Setter for the field feature.
void	AbstractInferredInteractionParticipant.setJAXBParticipantFeatureRef(Feature feature)	Sets the value of the participantFeatureRef property.

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

Classes in psidev.psi.mi.jami.xml.model.extension.xml253 with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractXmlEntity<F extends Feature>	Abstract class for XmlEntity
static class	AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature>
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features
class	AbstractXmlParticipant<I extends Interaction,F extends Feature>	Abstract class for XmlParticipant
static class	AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>
class	AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for XML Participant pool

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

Modifier and Type	Class	Description
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features
class	XmlFeature	Simple Xml implementation of a Feature
class	XmlFeatureEvidence	Xml implementation of a Feature
class	XmlFeatureEvidenceWrapper	Xml wrapper for feature evidences.
class	XmlFeatureWrapper	Xml wrapper for basic features
class	XmlModelledFeature	The xml implementation of a modelledFeature

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

Modifier and Type	Method	Description
List<Feature>	XmlParticipant.JAXBFeatureWrapper.getJAXBFeatures()
ExtendedPsiXmlFeature<Participant,Feature>	XmlFeatureWrapper.getWrappedFeature()	getWrappedFeature.
ParticipantCandidate<ParticipantPool,Feature>	XmlParticipantCandidateWrapper.getWrappedParticipant()	getWrappedParticipant.
ExtendedPsiXmlParticipant<Interaction,Feature>	XmlParticipantWrapper.getWrappedParticipant()	getWrappedParticipant.

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

Classes in psidev.psi.mi.jami.xml.model.extension.xml254 with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractXmlEntity<F extends Feature>	Abstract class for XmlEntity
static class	AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature>
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features
class	AbstractXmlParticipant<I extends Interaction,F extends Feature>	Abstract class for XmlParticipant
static class	AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>
class	AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for XML Participant pool

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

Modifier and Type	Class	Description
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features
class	XmlFeature	Simple Xml implementation of a Feature
class	XmlFeatureEvidence	Xml implementation of a Feature
class	XmlFeatureEvidenceWrapper	Xml wrapper for feature evidences.
class	XmlFeatureWrapper	Xml wrapper for basic features
class	XmlModelledFeature	The xml implementation of a modelledFeature

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

Modifier and Type	Method	Description
List<Feature>	XmlParticipant.JAXBFeatureWrapper.getJAXBFeatures()
ExtendedPsiXmlFeature<Participant,Feature>	XmlFeatureWrapper.getWrappedFeature()	getWrappedFeature.
ParticipantCandidate<ParticipantPool,Feature>	XmlParticipantCandidateWrapper.getWrappedParticipant()	getWrappedParticipant.
ExtendedPsiXmlParticipant<Interaction,Feature>	XmlParticipantWrapper.getWrappedParticipant()	getWrappedParticipant.

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

Classes in psidev.psi.mi.jami.xml.model.extension.xml300 with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractXmlEntity<F extends Feature>	Abstract class for XmlEntity
static class	AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature>
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features
class	AbstractXmlParticipant<I extends Interaction,F extends Feature>	Abstract class for XmlParticipant
static class	AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>
class	AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for XML Participant pool

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

Modifier and Type	Class	Description
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features
class	XmlFeature	Simple Xml implementation of a Feature
class	XmlFeatureEvidence	Xml implementation of a Feature
class	XmlFeatureEvidenceWrapper	Xml wrapper for feature evidences.
class	XmlFeatureWrapper	Xml wrapper for basic features
class	XmlModelledFeature	The xml implementation of a modelledFeature

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

Modifier and Type	Method	Description
List<Feature>	XmlParticipant.JAXBFeatureWrapper.getJAXBFeatures()
ExtendedPsiXmlFeature<Participant,Feature>	XmlFeatureWrapper.getWrappedFeature()	getWrappedFeature.
ParticipantCandidate<ParticipantPool,Feature>	XmlParticipantCandidateWrapper.getWrappedParticipant()	getWrappedParticipant.
ExtendedPsiXmlParticipant<Interaction,Feature>	XmlParticipantWrapper.getWrappedParticipant()	getWrappedParticipant.

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

Classes in psidev.psi.mi.jami.xml.model.reference with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractFeatureRef<E extends Entity,F extends Feature>	Abstract feature reference

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

Modifier and Type	Class	Description
class	AbstractFeatureRef<E extends Entity,F extends Feature>	Abstract feature reference

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

Classes in psidev.psi.mi.jami.xml.model.reference.xml253 with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractEntityRef<T extends Feature>	Abstract entity reference
class	AbstractParticipantRef<I extends Interaction,T extends Feature>	Abstract participant reference

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

Classes in psidev.psi.mi.jami.xml.model.reference.xml254 with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractEntityRef<T extends Feature>	Abstract entity reference
class	AbstractParticipantRef<I extends Interaction,T extends Feature>	Abstract participant reference

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

Classes in psidev.psi.mi.jami.xml.model.reference.xml300 with type parameters of type Feature

Modifier and Type	Class	Description
class	AbstractEntityRef<T extends Feature>	Abstract entity reference
class	AbstractParticipantRef<I extends Interaction,T extends Feature>	Abstract participant reference