Uses of Interface
psidev.psi.mi.jami.model.Interaction
-
-
Uses of Interaction in psidev.psi.mi.jami.analysis.graph
Classes in psidev.psi.mi.jami.analysis.graph with type parameters of type Interaction Modifier and Type Class Description classBindingSiteCliqueFinder<I extends Interaction,F extends Feature>The BindingSiteClique finder is an extension of BronKerboschCliqueFinder.classFeatureGraphBuilder<I extends Interaction,F extends Feature>This class will create a graph from one to several interactions. -
Uses of Interaction in psidev.psi.mi.jami.binary
Subinterfaces of Interaction in psidev.psi.mi.jami.binary Modifier and Type Interface Description interfaceBinaryInteraction<T extends Participant>A Binary interaction is an interaction only composed of two participants.interfaceBinaryInteractionEvidenceA BinaryInteractionEvidence is an InteractionEvidence with only two participantsinterfaceModelledBinaryInteractionA ModelledBinary interaction is a ModelledInteraction with only two participants -
Uses of Interaction in psidev.psi.mi.jami.binary.expansion
Classes in psidev.psi.mi.jami.binary.expansion with type parameters of type Interaction Modifier and Type Class Description classAbstractBipartiteExpansion<T extends Interaction,B extends BinaryInteraction>Abstract class for BipartiteExpansion.classAbstractComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>Abstract class for ComplexExpansionMethod.classAbstractMatrixExpansion<T extends Interaction,B extends BinaryInteraction>Abstract class for Matrix expansionclassAbstractSpokeExpansion<T extends Interaction,B extends BinaryInteraction>Abstract class for SpokeExpansioninterfaceComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>The method by which complex n-ary data is expanded into binary data.Methods in psidev.psi.mi.jami.binary.expansion with parameters of type Interaction Modifier and Type Method Description protected ParticipantSpokeExpansion. collectBestBaitForSpokeExpansion(Interaction interaction)collectBestBaitForSpokeExpansionprotected BinaryInteractionBipartiteExpansion. createBinaryInteraction(Interaction interaction, Participant c1, Participant c2)createBinaryInteractionprotected <P extends Participant>
BinaryInteractionMatrixExpansion. createBinaryInteraction(Interaction interaction, P c1, P c2)createBinaryInteractionprotected BinaryInteractionSpokeExpansion. createBinaryInteraction(Interaction interaction, Participant c1, Participant c2)createBinaryInteractionprotected Participant[]MatrixExpansion. createParticipantsArray(Interaction interaction)createParticipantsArrayCollection<BinaryInteraction>BipartiteExpansion. expand(Interaction interaction)expandCollection<BinaryInteraction>MatrixExpansion. expand(Interaction interaction)expandCollection<BinaryInteraction>SpokeExpansion. expand(Interaction interaction)expandprotected StringAbstractBipartiteExpansion. generateComplexName(Interaction interaction)generateComplexName -
Uses of Interaction in psidev.psi.mi.jami.binary.impl
Classes in psidev.psi.mi.jami.binary.impl with type parameters of type Interaction Modifier and Type Class Description classAbstractBinaryInteractionWrapper<I extends Interaction<T>,T extends Participant>Abstract class for binary interactions that wrap an Interaction.Classes in psidev.psi.mi.jami.binary.impl that implement Interaction Modifier and Type Class Description classAbstractBinaryInteraction<T extends Participant>Abstract class for BinaryInteraction.classAbstractBinaryInteractionWrapper<I extends Interaction<T>,T extends Participant>Abstract class for binary interactions that wrap an Interaction.classBinaryInteractionEvidenceWrapperA wrapper for InteractionEvidence which contains two participantsclassBinaryInteractionWrapperBinary Wrapper for an InteractionclassDefaultBinaryInteractionDefault implementation for BinaryInteraction Note: the methods equals and hashCode have not been overridden.classDefaultBinaryInteractionEvidenceDefault implementation for BinaryInteractionEvidenceclassDefaultModelledBinaryInteractionDefault implementation for ModelledBinaryInteractionclassDefaultNamedBinaryInteractionDefault implementation of a named binary interactionclassDefaultNamedBinaryInteractionEvidenceDefault implementation of a Named binary interaction evidenceclassDefaultNamedModelledBinaryInteractionDefault implementation for Named modelled binary interactionclassModelledBinaryInteractionWrapperA wrapper for ModelledInteraction which contains two participantsConstructors in psidev.psi.mi.jami.binary.impl with parameters of type Interaction Constructor Description BinaryInteractionWrapper(Interaction interaction)Constructor for BinaryInteractionWrapper.BinaryInteractionWrapper(Interaction interaction, CvTerm complexExpansion)Constructor for BinaryInteractionWrapper. -
Uses of Interaction in psidev.psi.mi.jami.commons
Method parameters in psidev.psi.mi.jami.commons with type arguments of type Interaction Modifier and Type Method Description Map<String,Object>MIWriterOptionFactory. getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Interaction> interactionSet, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)Create the options for the expanded PSI-XML InteractionWriter.Map<String,Object>MIWriterOptionFactory. getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)Create the options for the compact PSI-XML InteractionWriter. -
Uses of Interaction in psidev.psi.mi.jami.crosslink.extension
Subinterfaces of Interaction in psidev.psi.mi.jami.crosslink.extension Modifier and Type Interface Description interfaceCrosslinkCsvInteractionInteraction evidence extension from crosslinking CSV filesClasses in psidev.psi.mi.jami.crosslink.extension that implement Interaction Modifier and Type Class Description classCsvBinaryInteractionEvidenceCrosslink CSV implementation of BinaryInteractionEvidenceclassCsvInteractionEvidenceCSV extension for InteractionEvidence -
Uses of Interaction in psidev.psi.mi.jami.crosslink.extension.datasource
Methods in psidev.psi.mi.jami.crosslink.extension.datasource with parameters of type Interaction Modifier and Type Method Description voidAbstractCsvSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.voidAbstractCsvStreamSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.voidCsvMixedEvidenceSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.voidCsvNaryEvidenceSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants. -
Uses of Interaction in psidev.psi.mi.jami.datasource
Classes in psidev.psi.mi.jami.datasource with type parameters of type Interaction Modifier and Type Interface Description interfaceInteractionSource<T extends Interaction>A Data source of interactions.interfaceInteractionStream<T extends Interaction>A Data source of interactions giving only a stream of interactions.interfaceInteractionWriter<T extends Interaction>The InteractionWriter can write interactions in a datasource (files, database) -
Uses of Interaction in psidev.psi.mi.jami.enricher
Classes in psidev.psi.mi.jami.enricher with type parameters of type Interaction Modifier and Type Interface Description interfaceInteractionEnricher<I extends Interaction>The enricher for Interactions which can enrich a single interaction or a collection. -
Uses of Interaction in psidev.psi.mi.jami.enricher.impl.full
Classes in psidev.psi.mi.jami.enricher.impl.full with type parameters of type Interaction Modifier and Type Class Description classFullInteractionEnricher<I extends Interaction>Full enricher for interactionsclassFullInteractionUpdater<I extends Interaction>Full updater of interaction -
Uses of Interaction in psidev.psi.mi.jami.enricher.impl.minimal
Classes in psidev.psi.mi.jami.enricher.impl.minimal with type parameters of type Interaction Modifier and Type Class Description classMinimalInteractionEnricher<I extends Interaction>The enricher for Interactions which can enrich a single interaction or a collection.classMinimalInteractionUpdater<I extends Interaction>The enricher for Interactions which can enrich a single interaction or a collection. -
Uses of Interaction in psidev.psi.mi.jami.enricher.listener
Classes in psidev.psi.mi.jami.enricher.listener with type parameters of type Interaction Modifier and Type Interface Description interfaceInteractionEnricherListener<I extends Interaction>Listener for interaction enrichment -
Uses of Interaction in psidev.psi.mi.jami.enricher.listener.impl
Classes in psidev.psi.mi.jami.enricher.listener.impl with type parameters of type Interaction Modifier and Type Class Description classInteractionEnricherListenerManager<I extends Interaction>A manager for listeners which holds a list of listeners. -
Uses of Interaction in psidev.psi.mi.jami.enricher.listener.impl.log
Classes in psidev.psi.mi.jami.enricher.listener.impl.log with type parameters of type Interaction Modifier and Type Class Description classInteractionEnricherLogger<I extends Interaction>A logging listener. -
Uses of Interaction in psidev.psi.mi.jami.enricher.listener.impl.writer
Classes in psidev.psi.mi.jami.enricher.listener.impl.writer with type parameters of type Interaction Modifier and Type Class Description classInteractionEnricherStatisticsWriter<I extends Interaction>A statistics logger which records changes made by the enricher. -
Uses of Interaction in psidev.psi.mi.jami.enricher.util
Methods in psidev.psi.mi.jami.enricher.util with parameters of type Interaction Modifier and Type Method Description static <P extends Participant>
voidEnricherUtils. mergeParticipants(Interaction termToEnrich, Collection<P> toEnrichParticipants, Collection<P> fetchedParticipants, boolean remove, InteractionChangeListener interactionListener, ParticipantEnricher participantEnricher)mergeParticipants. -
Uses of Interaction in psidev.psi.mi.jami.examples.core
Methods in psidev.psi.mi.jami.examples.core that return Interaction Modifier and Type Method Description protected static InteractionCreateRogidAndRigid. createInteraction()createInteraction.protected static InteractionComplexExpansionWithJami. createInteractionWithBait()createInteractionWithBait.protected static InteractionBuildBindingSitesCliqueGraph. createInteractionWithLinkedFeatures()createInteractionWithLinkedFeatures. -
Uses of Interaction in psidev.psi.mi.jami.factory
Methods in psidev.psi.mi.jami.factory with type parameters of type Interaction Modifier and Type Method Description <I extends Interaction>
InteractionStream<I>MIDataSourceFactory. getInteractionSourceWith(Map<String,Object> requiredOptions)getInteractionSourceWithMethods in psidev.psi.mi.jami.factory that return types with arguments of type Interaction Modifier and Type Method Description ComplexExpansionMethod<Interaction,BinaryInteraction>ComplexExpansionFactory. createDefaultComplexExpansion(ComplexExpansionType type)Create an instance of complex expansion that suits the ComplexExpansionType and can deal with any kind of interactions (modelled, evidence)ComplexExpansionMethod<Interaction,BinaryInteraction>DefaultComplexExpansionFactory. createDefaultComplexExpansion(ComplexExpansionType type)Create an instance of complex expansion that suits the ComplexExpansionType and can deal with any kind of interactions (modelled, evidence)Methods in psidev.psi.mi.jami.factory with parameters of type Interaction Modifier and Type Method Description BinaryInteractionBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionDefaultBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionBinaryInteractionFactory. createBinaryInteractionWrapperFrom(Interaction interaction)Creates a BinaryInteraction that wraps the given interactionBinaryInteractionDefaultBinaryInteractionFactory. createBinaryInteractionWrapperFrom(Interaction interaction)Creates a BinaryInteraction that wraps the given interactionBinaryInteractionBinaryInteractionFactory. createSelfBinaryInteractionFrom(Interaction interaction)Create a binary interaction representing a self interactionBinaryInteractionDefaultBinaryInteractionFactory. createSelfBinaryInteractionFrom(Interaction interaction)Create a binary interaction representing a self interaction -
Uses of Interaction in psidev.psi.mi.jami.html
Classes in psidev.psi.mi.jami.html with type parameters of type Interaction Modifier and Type Class Description classAbstractMIHtmlWriter<T extends Interaction,P extends Participant,F extends Feature>Abstract class for MI HTML writerMethods in psidev.psi.mi.jami.html with parameters of type Interaction Modifier and Type Method Description voidMIHtmlWriter. write(Interaction interaction)writeprotected voidLightMIHtmlWriter. writeConfidences(Interaction interaction)writeConfidencesprotected voidMIHtmlWriter. writeConfidences(Interaction interaction)writeConfidencesprotected voidLightMIHtmlWriter. writeCooperativeEffects(Interaction interaction)writeCooperativeEffectsprotected voidMIHtmlWriter. writeCooperativeEffects(Interaction interaction)writeCooperativeEffectsprotected voidLightMIHtmlWriter. writeExperiment(Interaction interaction)writeExperimentprotected voidMIHtmlWriter. writeExperiment(Interaction interaction)writeExperimentprotected voidLightMIHtmlWriter. writeGeneralProperties(Interaction interaction)writeGeneralPropertiesprotected voidMIHtmlWriter. writeGeneralProperties(Interaction interaction)writeGeneralPropertiesprotected voidAbstractMIHtmlWriter. writeInteractionAnchor(Interaction interaction)writeInteractionAnchorprotected voidLightMIHtmlWriter. writeParameters(Interaction interaction)writeParametersprotected voidMIHtmlWriter. writeParameters(Interaction interaction)writeParametersMethod parameters in psidev.psi.mi.jami.html with type arguments of type Interaction Modifier and Type Method Description voidMIHtmlWriter. write(Collection<? extends Interaction> interactions)writevoidMIHtmlWriter. write(Iterator<? extends Interaction> interactions)Writes Interaction objects using iterator -
Uses of Interaction in psidev.psi.mi.jami.imex
Methods in psidev.psi.mi.jami.imex with parameters of type Interaction Modifier and Type Method Description protected voidImexInteractionUpdater. processAnnotations(Interaction objectToEnrich, Interaction objectSource)processAnnotations.protected voidImexInteractionUpdater. processChecksums(Interaction objectToEnrich, Interaction objectSource)processChecksums.protected voidImexInteractionUpdater. processCreatedDate(Interaction objectToEnrich, Interaction objectSource)processCreatedDate.protected voidImexInteractionUpdater. processIdentifiers(Interaction objectToEnrich, Interaction objectSource)processIdentifiers.protected voidImexInteractionUpdater. processInteractionType(Interaction interactionToEnrich)processInteractionType.protected voidImexInteractionUpdater. processInteractionType(Interaction objectToEnrich, Interaction objectSource)processInteractionType.protected voidImexInteractionUpdater. processOtherProperties(Interaction interactionToEnrich)The strategy used for enriching the interaction.protected voidImexInteractionUpdater. processParticipants(Interaction interactionToEnrich)processParticipants.protected voidImexInteractionUpdater. processParticipants(Interaction objectToEnrich, Interaction objectSource)processParticipants.protected voidImexInteractionUpdater. processRigid(Interaction interactionToEnrich)processRigid.protected voidImexInteractionUpdater. processShortName(Interaction objectToEnrich, Interaction objectSource)processShortName.protected voidImexInteractionUpdater. processUpdateDate(Interaction objectToEnrich, Interaction objectSource)processUpdateDate.protected voidImexInteractionUpdater. processXrefs(Interaction objectToEnrich, Interaction objectSource)processXrefs. -
Uses of Interaction in psidev.psi.mi.jami.json
Methods in psidev.psi.mi.jami.json with parameters of type Interaction Modifier and Type Method Description static String[]MIJsonUtils. extractInteractionId(Xref ref, Interaction interaction)extractInteractionId. -
Uses of Interaction in psidev.psi.mi.jami.json.binary
Classes in psidev.psi.mi.jami.json.binary with type parameters of type Interaction Modifier and Type Class Description classAbstractMIJsonWriter<I extends Interaction,B extends BinaryInteraction>The jsonWriter which writes the interactions -
Uses of Interaction in psidev.psi.mi.jami.json.elements
Classes in psidev.psi.mi.jami.json.elements with type parameters of type Interaction Modifier and Type Class Description classSimpleJsonInteractionWriter<I extends Interaction>Json writer for interactions -
Uses of Interaction in psidev.psi.mi.jami.json.nary
Classes in psidev.psi.mi.jami.json.nary with type parameters of type Interaction Modifier and Type Class Description classAbstractMIJsonWriter<I extends Interaction>Abstract JSON writer for interactions (n-ary json format)Methods in psidev.psi.mi.jami.json.nary with parameters of type Interaction Modifier and Type Method Description voidMIJsonWriter. write(Interaction interaction)write. -
Uses of Interaction in psidev.psi.mi.jami.listener
Classes in psidev.psi.mi.jami.listener with type parameters of type Interaction Modifier and Type Interface Description interfaceInteractionChangeListener<I extends Interaction>Listener for changes in interactionMethods in psidev.psi.mi.jami.listener with parameters of type Interaction Modifier and Type Method Description voidMIFileParserListener. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants. -
Uses of Interaction in psidev.psi.mi.jami.listener.impl
Classes in psidev.psi.mi.jami.listener.impl with type parameters of type Interaction Modifier and Type Class Description classInteractionChangeLogger<T extends Interaction>This listener will just interaction change eventsMethods in psidev.psi.mi.jami.listener.impl with parameters of type Interaction Modifier and Type Method Description voidMIFileParserCompositeListener. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.voidMIFileParserLogger. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants. -
Uses of Interaction in psidev.psi.mi.jami.model
Classes in psidev.psi.mi.jami.model with type parameters of type Interaction Modifier and Type Interface Description interfaceNamedParticipant<I extends Interaction,F extends Feature>A named entity is an entity having a short name and a fullname in addition to aliases.interfaceParticipant<I extends Interaction,F extends Feature>Participant identified in an interactioninterfaceParticipantPool<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 interchangeableSubinterfaces of Interaction in psidev.psi.mi.jami.model Modifier and Type Interface Description interfaceComplexAn interactor composed of interacting molecules that can be copurified.interfaceInteractionEvidenceInteraction involving one to several molecules supported by experiments.interfaceModelledInteractionAn interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...interfaceNamedInteraction<T extends Participant>A named interaction is an interaction having a fullname and aliases in addition to a shortname. -
Uses of Interaction in psidev.psi.mi.jami.model.impl
Classes in psidev.psi.mi.jami.model.impl with type parameters of type Interaction Modifier and Type Class Description classAbstractParticipant<I extends Interaction,F extends Feature>Abstract class for ParticipantclassAbstractParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>Abstract class for Participant poolClasses in psidev.psi.mi.jami.model.impl that implement Interaction Modifier and Type Class Description classAbstractInteraction<T extends Participant>Abstract class for interactionsclassDefaultComplexDefault implementation for complexes Notes: The equals and hashcode methods have NOT been overridden because the Complex object is a complex object.classDefaultInteractionDefault implementation for interaction Notes: The equals and hashcode methods have NOT been overridden because the interaction object is a complex object.classDefaultInteractionEvidenceDefault implementation for InteractionEvidence Notes: The equals and hashcode methods have NOT been overridden because the InteractionEvidence object is a complex object.classDefaultModelledInteractionDefault implemntation for ModelledInteraction Notes: The equals and hashcode methods have NOT been overridden because the ModelledInteraction object is a complex object.classDefaultNamedInteractionDefault implementation for Named interactionclassDefaultNamedInteractionEvidenceDefault implementation for Named InteractionEvidenceclassDefaultNamedModelledInteractionDefault implementation of Named modelled interaction -
Uses of Interaction in psidev.psi.mi.jami.tab.extension
Classes in psidev.psi.mi.jami.tab.extension that implement Interaction Modifier and Type Class Description classMitabBinaryInteractionA MitabBinaryInteraction is a binaryInteraction with a MitabSourceLocatorclassMitabBinaryInteractionEvidenceTODO comment thisclassMitabComplexMitab extension for Complex.classMitabInteractionMitab extension for Interaction It contains a SourceLocatorclassMitabInteractionEvidenceMitab extension for InteractionEvidenceclassMitabModelledBinaryInteractionA MitabBinaryInteraction is a modelled binaryInteraction with a MitabSourceLocatorclassMitabModelledInteractionMitab extension for ModelledInteraction. -
Uses of Interaction in psidev.psi.mi.jami.tab.extension.datasource
Classes in psidev.psi.mi.jami.tab.extension.datasource with type parameters of type Interaction Modifier and Type Class Description classAbstractMitabSource<T extends Interaction,P extends Participant,F extends Feature>Abstract class for an InteractionSource coming from a MITAB file.classAbstractMitabStreamSource<T extends Interaction,P extends Participant,F extends Feature>abstract class for Mitab datasource.interfaceMitabSource<I extends Interaction>Interface for MITAB sources that can parse full MITAB filesinterfaceMitabStreamSource<I extends Interaction>Interface for MITAB datasources that can stream MITAB filesMethods in psidev.psi.mi.jami.tab.extension.datasource that return types with arguments of type Interaction Modifier and Type Method Description protected Iterator<Interaction>LightMitabStreamSource. createMitabIterator()createMitabIterator.Collection<Interaction>DefaultMitabSource. getInteractions()getInteractions.Iterator<Interaction>DefaultMitabStreamSource. getInteractionsIterator()getInteractionsIterator.Methods in psidev.psi.mi.jami.tab.extension.datasource with parameters of type Interaction Modifier and Type Method Description voidAbstractMitabSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.voidAbstractMitabStreamSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.voidDefaultMitabStreamSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants. -
Uses of Interaction in psidev.psi.mi.jami.tab.io.iterator
Classes in psidev.psi.mi.jami.tab.io.iterator with type parameters of type Interaction Modifier and Type Class Description classAbstractMitabIterator<T extends Interaction,P extends Participant,F extends Feature>Abstract class for mitab iteratorConstructor parameters in psidev.psi.mi.jami.tab.io.iterator with type arguments of type Interaction Constructor Description MitabInteractionIterator(MitabLineParser<Interaction,Participant,Feature> lineParser)Constructor for MitabInteractionIterator. -
Uses of Interaction in psidev.psi.mi.jami.tab.io.parser
Classes in psidev.psi.mi.jami.tab.io.parser with type parameters of type Interaction Modifier and Type Class Description classAbstractInteractionLineParser<T extends Interaction,P extends Participant,F extends Feature>Abstract mitab line parserclassAbstractLightInteractionLineParser<T extends Interaction>Abstract class for InteractionLine parsersclassMitabLineParser<T extends Interaction,P extends Participant,F extends Feature>Methods in psidev.psi.mi.jami.tab.io.parser that return Interaction Modifier and Type Method Description protected InteractionInteractionLineParser. createInteraction()createInteraction.Methods in psidev.psi.mi.jami.tab.io.parser with parameters of type Interaction Modifier and Type Method Description protected voidInteractionLineParser. addParticipant(Participant participant, Interaction interaction)addParticipant.protected voidAbstractInteractionLineParser. createChecksumFromId(Interaction interaction, MitabXref ref)createChecksumFromId. -
Uses of Interaction in psidev.psi.mi.jami.tab.io.writer
Classes in psidev.psi.mi.jami.tab.io.writer with type parameters of type Interaction Modifier and Type Class Description classAbstractMitabWriter<T extends Interaction,B extends BinaryInteraction,P extends Participant>Abstract writer for Mitab 2.5.Methods in psidev.psi.mi.jami.tab.io.writer with parameters of type Interaction Modifier and Type Method Description voidDefaultMitabWriter. write(Interaction interaction)write.voidMitab25Writer. write(Interaction interaction)write.Method parameters in psidev.psi.mi.jami.tab.io.writer with type arguments of type Interaction Modifier and Type Method Description protected voidLightMitab25Writer. initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidMitab25Writer. initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)initialiseExpansionMethod. -
Uses of Interaction in psidev.psi.mi.jami.tab.io.writer.extended
Methods in psidev.psi.mi.jami.tab.io.writer.extended with parameters of type Interaction Modifier and Type Method Description voidMitab25Writer. write(Interaction interaction)write.Method parameters in psidev.psi.mi.jami.tab.io.writer.extended with type arguments of type Interaction Modifier and Type Method Description protected voidMitab25Writer. initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)initialiseExpansionMethod. -
Uses of Interaction in psidev.psi.mi.jami.utils
Methods in psidev.psi.mi.jami.utils with parameters of type Interaction Modifier and Type Method Description static BinaryInteractionInteractionUtils. createBinaryInteractionFrom(Interaction interaction)Create a BinaryInteractionWrapper from the given interaction which should contain not more than two participants.static BinaryInteractionInteractionUtils. createNewSelfBinaryInteractionFrom(Interaction interaction)Creates a new BinaryInteraction from the given interaction which should only contain one participant with a stoichiometry >= 2 or participant stoichiometry null and participant is not self/putative self.static Collection<Participant>InteractionUtils. extractParticipantWithCausalRelationships(Interaction interaction)This method can return all participants having causal relationships in an interactionstatic ComplexTypeInteractionUtils. findInteractionCategoryOf(Interaction interaction, boolean checkExperimentalRoleIfInteractionEvidence)The method will find the interactionCategory (binary, self, etc.) -
Uses of Interaction in psidev.psi.mi.jami.utils.clone
Methods in psidev.psi.mi.jami.utils.clone with parameters of type Interaction Modifier and Type Method Description static voidInteractorCloner. copyAndOverrideBasicComplexPropertiesWithInteractionProperties(Interaction source, Complex target)This method will copy basic properties from the Interaction source in the complex target.static voidInteractionCloner. copyAndOverrideBasicInteractionProperties(Interaction source, Interaction target, boolean createNewParticipant, boolean ignoreParticipants)This method will copy basic properties of interaction source in interaction target and will override all the other properties of Target interaction.static voidInteractionCloner. copyAndOverrideBasicParticipantsToBinary(Interaction source, BinaryInteraction target, boolean createNewParticipant, boolean self)This method will copy participants of interaction source in binary target. -
Uses of Interaction in psidev.psi.mi.jami.utils.comparator.interaction
Methods in psidev.psi.mi.jami.utils.comparator.interaction that return types with arguments of type Interaction Modifier and Type Method Description Comparator<Interaction>CuratedInteractionBaseComparator. getInteractionBaseComparator()Getter for the fieldinteractionBaseComparator.Comparator<Interaction>InteractionComparator. getInteractionBaseComparator()Getter for the fieldinteractionBaseComparator.Comparator<Interaction>InteractionEvidenceComparator. getInteractionBaseComparator()getInteractionBaseComparatorComparator<Interaction>ModelledInteractionComparator. getInteractionBaseComparator()Getter for the fieldinteractionBaseComparator.Methods in psidev.psi.mi.jami.utils.comparator.interaction with parameters of type Interaction Modifier and Type Method Description static booleanDefaultCuratedInteractionBaseComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultCuratedInteractionBaseComparator to know if two interactions are equals.static booleanDefaultCuratedInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultCuratedInteractionComparator to know if two interactions are equals.static booleanDefaultExactCuratedInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultExactCuratedInteractionComparator to know if two interactions are equals.static booleanDefaultExactInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultExactInteractionComparator to know if two interactions are equals.static booleanDefaultExactInteractionInteractorComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultExactInteractionInteractorComparator to know if two interactions are equals.static booleanDefaultInteractionBaseComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultInteractionBaseComparator to know if two interactions are equals.static booleanDefaultInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultInteractionComparator to know if two interactions are equals.static booleanDefaultInteractionInteractorComparator. areEquals(Interaction interaction1, Interaction interaction2)Use DefaultInteractionInteractorComparator to know if two interactions are equals.static booleanUnambiguousCuratedInteractionBaseComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousCuratedInteractionBaseComparator to know if two interactions are equals.static booleanUnambiguousCuratedInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousCuratedInteractionComparator to know if two interactions are equals.static booleanUnambiguousExactCuratedInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousExactCuratedInteractionComparator to know if two interactions are equals.static booleanUnambiguousExactInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousExactInteractionComparator to know if two interactions are equals.static booleanUnambiguousExactInteractionInteractorComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousExactInteractionInteractorComparator to know if two interactions are equals.static booleanUnambiguousInteractionBaseComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousInteractionBaseComparator to know if two interactions are equals.static booleanUnambiguousInteractionComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousInteractionComparator to know if two interactions are equals.static booleanUnambiguousInteractionInteractorComparator. areEquals(Interaction interaction1, Interaction interaction2)Use UnambiguousInteractionInteractorComparator to know if two interactions are equals.intCuratedInteractionBaseComparator. compare(Interaction interaction1, Interaction interaction2)It will first compare the basic properties of an interaction using AbstractInteractionBaseComparator.intInteractionBaseComparator. compare(Interaction interaction1, Interaction interaction2)It will first compare the interaction types using UnambiguousCvTermComparator.intInteractionComparator. compare(Interaction interaction1, Interaction interaction2)Modelled interactions come first, then experimental interactions.intInteractionInteractorComparator. compare(Interaction interaction1, Interaction interaction2)It will use a ParticipantInteractorComparator comparator for comparing the participants involved in the interaction.intUnambiguousCuratedInteractionBaseComparator. compare(Interaction interaction1, Interaction interaction2)It will first compare the basic properties of an interaction using AbstractInteractionBaseComparator.intUnambiguousCuratedInteractionComparator. compare(Interaction interaction1, Interaction interaction2)Experimental interactions come first, then allosteric interactions, then cooperative interactions, then modelled interactions.intUnambiguousExactCuratedInteractionComparator. compare(Interaction interaction1, Interaction interaction2)Modelled interactions come first and then experimental interactions - It uses UnambiguousExactCuratedInteractionEvidenceComparator to compare experimental interactions - It uses UnambiguousExactCuratedModelledInteractionComparator to compare modelled interactions - It uses UnambiguousCuratedInteractionBaseComparator to compare basic interaction propertiesintUnambiguousExactInteractionComparator. compare(Interaction interaction1, Interaction interaction2)Modelled interactions come first and then experimental interactions - It uses UnambiguousExactInteractionEvidenceComparator to compare experimental interactions - It uses UnambiguousExactModelledInteractionComparator to compare modelled interactions - It uses UnambiguousInteractionBaseComparator to compare basic interaction propertiesintUnambiguousExactInteractionInteractorComparator. compare(Interaction interaction1, Interaction interaction2)intUnambiguousInteractionComparator. compare(Interaction interaction1, Interaction interaction2)Modelled interactions come first, then experimental interactions.intUnambiguousInteractionInteractorComparator. compare(Interaction interaction1, Interaction interaction2)static intUnambiguousCuratedInteractionBaseComparator. hashCode(Interaction interaction)hashCodestatic intUnambiguousInteractionBaseComparator. hashCode(Interaction interaction)hashCodeConstructor parameters in psidev.psi.mi.jami.utils.comparator.interaction with type arguments of type Interaction Constructor Description CuratedInteractionBaseComparator(Comparator<Interaction> interactionBaseComparator)Constructor for CuratedInteractionBaseComparator.CuratedModelledInteractionComparator(CustomizableModelledParticipantComparator participantComparator, Comparator<Interaction> interactionComparator, Comparator<CvTerm> sourceComparator)Constructor for CuratedModelledInteractionComparator.InteractionComparator(Comparator<Interaction> interactionBaseComparator, ModelledInteractionComparator modelledInteractionComparator, InteractionEvidenceComparator experimentalInteractionComparator)Constructor for InteractionComparator.InteractionEvidenceComparator(CollectionComparator<ParticipantEvidence> participantComparator, Comparator<Interaction> interactionComparator, ExperimentComparator experimentComparator, CollectionComparator<Parameter> parameterComparator, CollectionComparator<VariableParameterValueSet> variableParameterValuesSetComparator)Constructor for InteractionEvidenceComparator.ModelledInteractionComparator(CollectionComparator<ModelledParticipant> participantComparator, Comparator<Interaction> interactionComparator)Constructor for ModelledInteractionComparator.ModelledInteractionComparator(CustomizableModelledParticipantComparator participantComparator, Comparator<Interaction> interactionComparator)Constructor for ModelledInteractionComparator. -
Uses of Interaction in psidev.psi.mi.jami.xml
Methods in psidev.psi.mi.jami.xml with parameters of type Interaction Modifier and Type Method Description voidXmlEntryContext. registerInteraction(int id, Interaction o)registerInteraction. -
Uses of Interaction in psidev.psi.mi.jami.xml.cache
Methods in psidev.psi.mi.jami.xml.cache that return Interaction Modifier and Type Method Description InteractionInMemoryPsiXmlCache. getInteraction(int id)getInteraction.InteractionPsiXmlFileIndexCache. getInteraction(int id)getInteraction.InteractionPsiXmlIdCache. getInteraction(int id)getInteraction.Methods in psidev.psi.mi.jami.xml.cache with parameters of type Interaction Modifier and Type Method Description intInMemoryIdentityObjectCache. extractIdForInteraction(Interaction 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 registeredintInMemoryLightIdentityObjectCache. extractIdForInteraction(Interaction 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 registeredintPsiXmlObjectCache. extractIdForInteraction(Interaction 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 registeredComplexInMemoryPsiXmlCache. registerComplexLoadedFrom(Interaction f)registerComplexLoadedFrom.ComplexPsiXmlFileIndexCache. registerComplexLoadedFrom(Interaction f)registerComplexLoadedFrom.ComplexPsiXmlIdCache. registerComplexLoadedFrom(Interaction f)registerComplexLoadedFrom.voidInMemoryPsiXmlCache. registerInteraction(int id, Interaction object)Register an interaction with an idvoidPsiXmlFileIndexCache. registerInteraction(int id, Interaction object)Register an interaction with an idvoidPsiXmlIdCache. registerInteraction(int id, Interaction object)Register an interaction with an id -
Uses of Interaction in psidev.psi.mi.jami.xml.io.iterator
Classes in psidev.psi.mi.jami.xml.io.iterator with type parameters of type Interaction Modifier and Type Class Description classAbstractXmlIterator<T extends Interaction>Abstract iterator for parsing xml interactionsConstructor parameters in psidev.psi.mi.jami.xml.io.iterator with type arguments of type Interaction Constructor Description XmlInteractionIterator(PsiXmlParser<Interaction> lineParser)Constructor for XmlInteractionIterator. -
Uses of Interaction in psidev.psi.mi.jami.xml.io.parser
Classes in psidev.psi.mi.jami.xml.io.parser with type parameters of type Interaction Modifier and Type Class Description classAbstractFullPsiXmlParser<T extends Interaction>This class if for parser that will load the all file in memoryclassAbstractPsixmlBinaryParser<T extends Interaction,B extends BinaryInteraction>Abstract class for a binary interaction parserclassAbstractPsiXmlParser<T extends Interaction>Parser for PSI-XML Returns an Iterator of interactions.interfaceFullPsiXmlParser<T extends Interaction>Full parser that loads the all entry set.interfacePsiXmlParser<T extends Interaction>Interface for PsiXmlParserMethods in psidev.psi.mi.jami.xml.io.parser that return types with arguments of type Interaction Modifier and Type Method Description AbstractEntrySet<AbstractBaseEntry<Interaction>>FullXmlBinaryParser. getEntrySet()getEntrySet.AbstractEntrySet<AbstractBaseEntry<Interaction<? extends Participant>>>LightFullXmlBinaryParser. getEntrySet()getEntrySet.protected ComplexExpansionMethod<Interaction,BinaryInteraction>FullXmlBinaryParser. initialiseDefaultExpansionMethod()initialiseDefaultExpansionMethod.protected ComplexExpansionMethod<Interaction,BinaryInteraction>LightFullXmlBinaryParser. initialiseDefaultExpansionMethod()initialiseDefaultExpansionMethod.protected ComplexExpansionMethod<Interaction,BinaryInteraction>LightXmlBinaryParser. initialiseDefaultExpansionMethod()initialiseDefaultExpansionMethod.protected ComplexExpansionMethod<Interaction,BinaryInteraction>XmlBinaryParser. initialiseDefaultExpansionMethod()initialiseDefaultExpansionMethod. -
Uses of Interaction in psidev.psi.mi.jami.xml.io.writer
Classes in psidev.psi.mi.jami.xml.io.writer with type parameters of type Interaction Modifier and Type Class Description classAbstractXmlWriter<T extends Interaction>Abstract class for XML writer of interactionsMethods in psidev.psi.mi.jami.xml.io.writer that return types with arguments of type Interaction Modifier and Type Method Description protected Set<Interaction>AbstractXmlWriter. getProcessedInteractions()Getter for the fieldprocessedInteractions.Methods in psidev.psi.mi.jami.xml.io.writer with parameters of type Interaction Modifier and Type Method Description voidDefaultXmlWriter. write(Interaction interaction)write.Method parameters in psidev.psi.mi.jami.xml.io.writer with type arguments of type Interaction Modifier and Type Method Description voidAbstractXmlWriter. setInteractionSet(Set<Interaction> processedInteractions)setInteractionSet. -
Uses of Interaction in psidev.psi.mi.jami.xml.io.writer.compact
Classes in psidev.psi.mi.jami.xml.io.writer.compact with type parameters of type Interaction Modifier and Type Class Description classAbstractCompactXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence>Abstract class for a compact PSI-XML writer of mixed interactionsclassAbstractCompactXmlWriter<T extends Interaction>Abstract class for Compact XML writers.Methods in psidev.psi.mi.jami.xml.io.writer.compact with parameters of type Interaction Modifier and Type Method Description protected voidLightCompactXmlNamedWriter. registerAvailabilities(Interaction interaction)registerAvailabilities.protected voidLightCompactXmlWriter. registerAvailabilities(Interaction interaction)registerAvailabilities.protected voidLightCompactXmlNamedWriter. registerExperiment(Interaction interaction)registerExperiment.protected voidLightCompactXmlWriter. registerExperiment(Interaction interaction)registerExperiment.Method parameters in psidev.psi.mi.jami.xml.io.writer.compact with type arguments of type Interaction Modifier and Type Method Description voidAbstractCompactXmlMixWriter. setInteractionSet(Set<Interaction> processedInteractions)setInteractionSet. -
Uses of Interaction 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 Interaction Modifier and Type Method Description protected voidLightCompactXmlWriter. registerAvailabilities(Interaction interaction)registerAvailabilities.protected voidLightCompactXmlWriter. registerExperiment(Interaction interaction)registerExperiment. -
Uses of Interaction in psidev.psi.mi.jami.xml.io.writer.elements
Classes in psidev.psi.mi.jami.xml.io.writer.elements with type parameters of type Interaction Modifier and Type Interface Description interfacePsiXmlExtendedInteractionWriter<T extends Interaction>Interface for interaction writers writing extensionsinterfacePsiXmlInteractionWriter<T extends Interaction>Interface for PSI-XML interaction writers that have to write an experiment in XML even if the interaction does not have any experimental details -
Uses of Interaction 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 Interaction Modifier and Type Class Description classAbstractXmlInteractionWriter<T extends Interaction,P extends Participant>Abstract writer of interaction -
Uses of Interaction 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 Interaction Modifier and Type Class Description classAbstractXmlInteractionWriter<T extends Interaction>Abstract writer of interaction in PSI-XML 2.5 -
Uses of Interaction 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 Interaction Modifier and Type Method Description protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments.protected voidXmlNamedInteractionWriter. writeNames(Interaction object)writeNames. -
Uses of Interaction 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 Interaction Modifier and Type Method Description protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments.protected voidXmlNamedInteractionWriter. writeNames(Interaction object)writeNames. -
Uses of Interaction 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 Interaction Modifier and Type Method Description protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments. -
Uses of Interaction 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 Interaction Modifier and Type Method Description protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments. -
Uses of Interaction 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 Interaction Modifier and Type Class Description classAbstractXmlInteractionWriter<I extends Interaction>Abstract class for extended XML 2.5 interaction writer -
Uses of Interaction in psidev.psi.mi.jami.xml.io.writer.expanded
Classes in psidev.psi.mi.jami.xml.io.writer.expanded with type parameters of type Interaction Modifier and Type Class Description classAbstractExpandedXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence>Abstract class for an expanded PSI-XML writer of mixed interactionsclassAbstractExpandedXmlWriter<T extends Interaction>Abstract class for expanded PSI-xml writersMethod parameters in psidev.psi.mi.jami.xml.io.writer.expanded with type arguments of type Interaction Modifier and Type Method Description voidAbstractExpandedXmlMixWriter. setInteractionSet(Set<Interaction> processedInteractions)setInteractionSet. -
Uses of Interaction in psidev.psi.mi.jami.xml.model
Classes in psidev.psi.mi.jami.xml.model with type parameters of type Interaction Modifier and Type Class Description classAbstractBaseEntry<T extends Interaction>Abstract class for Entry -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension
Classes in psidev.psi.mi.jami.xml.model.extension with type parameters of type Interaction Modifier and Type Interface Description interfaceExtendedPsiXmlParticipant<I extends Interaction,F extends Feature>Extended participant for PSI-XML 2,5 standardsSubinterfaces of Interaction in psidev.psi.mi.jami.xml.model.extension Modifier and Type Interface Description interfaceExtendedPsiXmlInteraction<T extends Participant>Extended interaction for PSI-XML 2,5 standardsinterfaceExtendedPsiXmlInteractionEvidenceExtended interaction evidence for PSI-XML 2,5 standardsinterfaceExtendedPsiXmlModelledInteractionExtended modelled interaction for PSI-XML 2,5 standardsinterfacePsiXmlInteraction<T extends Participant>Interaction for PSI-XML which contains the entry -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.binary
Classes in psidev.psi.mi.jami.xml.model.extension.binary that implement Interaction Modifier and Type Class Description classAbstractExtendedXmlBinaryInteraction<P extends Participant>Abstract class for xml binary interactionsclassAbstractXmlBinaryInteraction<P extends Participant>Abstract class for xml binary interactionsclassAbstractXmlBinaryInteractionEvidenceAbstract class for Xml BinaryInteractionEvidenceclassXmlBinaryInteractionXml implementation of binary interactionclassXmlBinaryInteractionEvidenceWrapperXml implementation of BinaryInteractionWrapper with a source locatorclassXmlBinaryInteractionWrapperWrapper for ModelledBinaryInteractionclassXmlModelledBinaryInteractionXml implementation of ModelledInteractionclassXmlModelledBinaryInteractionWrapperWrapper for Xml binary interactions -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.binary.xml253
Classes in psidev.psi.mi.jami.xml.model.extension.binary.xml253 that implement Interaction Modifier and Type Class Description classXmlBinaryInteractionEvidenceXml implementation of BinaryInteractionEvidence -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.binary.xml254
Classes in psidev.psi.mi.jami.xml.model.extension.binary.xml254 that implement Interaction Modifier and Type Class Description classXmlBinaryInteractionEvidenceXml implementation of BinaryInteractionEvidence -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.binary.xml30
Classes in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that implement Interaction Modifier and Type Class Description classXmlBinaryInteractionEvidenceXml implementation of BinaryInteractionEvidenceclassXmlBinaryInteractionEvidenceWrapperXml implementation of BinaryInteractionWrapper with a source locatorclassXmlModelledBinaryInteractionXml implementation of ModelledInteractionclassXmlModelledBinaryInteractionWrapperWrapper for Xml binary interactions -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.datasource
Classes in psidev.psi.mi.jami.xml.model.extension.datasource with type parameters of type Interaction Modifier and Type Class Description classAbstractPsiXmlBinarySource<T extends Interaction,B extends BinaryInteraction>Abstract class for Psi-XML binary interaction data source which loads the full interaction datasetclassAbstractPsiXmlBinaryStream<T extends Interaction,B extends BinaryInteraction>Abstract class for binary interaction datasourcesclassAbstractPsiXmlSource<T extends Interaction>Abstract class for a PSI-XML datasource that loads the full interaction datasetclassAbstractPsiXmlStream<T extends Interaction>Abstract class for psiXml data sourceinterfacePsiXmlSource<I extends Interaction>Interface for PSI-MI XML sources that can parse full PSI-MI XML filesinterfacePsiXmlStreamSource<I extends Interaction>Interface for PSI-MI XML datasources that can stream PSI-MI XML filesMethods in psidev.psi.mi.jami.xml.model.extension.datasource that return types with arguments of type Interaction Modifier and Type Method Description protected Iterator<Interaction>LightXmlStreamSource. createXmlIterator()createXmlIterator.protected Iterator<Interaction>XmlStreamSource. createXmlIterator()createXmlIterator.Collection<Interaction>DefaultPsiXmlSource. getInteractions()getInteractions.Iterator<Interaction>DefaultPsiXmlStreamSource. getInteractionsIterator()getInteractionsIterator.Methods in psidev.psi.mi.jami.xml.model.extension.datasource with parameters of type Interaction Modifier and Type Method Description voidAbstractPsiXmlStream. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.voidDefaultPsiXmlStreamSource. onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)Listen to an event fired when an interaction is read and does not have any participants.Method parameters in psidev.psi.mi.jami.xml.model.extension.datasource with type arguments of type Interaction Modifier and Type Method Description protected voidAbstractPsiXmlBinarySource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidAbstractPsiXmlBinaryStream. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected abstract voidAbstractPsiXmlStream. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidLightXmlSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidLightXmlStreamSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlComplexSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlComplexStreamSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlEvidenceSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlEvidenceStreamSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlModelledSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlModelledStreamSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod.protected voidXmlStreamSource. initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)initialiseExpansionMethod. -
Uses of Interaction 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 Interaction Modifier and Type Method Description BinaryInteractionXmlBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionXmlBinaryInteractionFactory. createBinaryInteractionWrapperFrom(Interaction interaction)Creates a BinaryInteraction that wraps the given interactionBinaryInteractionXmlBinaryInteractionFactory. createSelfBinaryInteractionFrom(Interaction interaction)Create a binary interaction representing a self interaction -
Uses of Interaction 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 Interaction Modifier and Type Method Description BinaryInteractionXmlBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionXmlBinaryInteractionFactory. createBinaryInteractionWrapperFrom(Interaction interaction)Creates a BinaryInteraction that wraps the given interactionBinaryInteractionXmlBinaryInteractionFactory. createSelfBinaryInteractionFrom(Interaction interaction)Create a binary interaction representing a self interaction -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.xml253
Classes in psidev.psi.mi.jami.xml.model.extension.xml253 with type parameters of type Interaction Modifier and Type Class Description classAbstractXmlParticipant<I extends Interaction,F extends Feature>Abstract class for XmlParticipantstatic classAbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>classAbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>Abstract class for XML Participant poolClasses in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Interaction Modifier and Type Class Description classAbstractPsiXmlInteraction<T extends Participant>Abstract class for xml interactions implementing ExtendedPsiXmlInteraction interfaceclassAbstractXmlBasicInteractionXml implementation of interactionclassAbstractXmlComplexXml implementation for complexclassAbstractXmlInteraction<T extends Participant>Abstract class for xml interactionsclassAbstractXmlInteractionEvidenceXml implementation of InteractionEvidenceclassAbstractXmlModelledInteractionXml implementation of ModelledInteractionclassDefaultXmlBasicInteractionXml implementation of interactionclassDefaultXmlComplexXml implementation for complexclassDefaultXmlInteractionEvidenceXml implementation of InteractionEvidenceclassDefaultXmlModelledInteractionXml implementation of ModelledInteractionclassXmlBasicInteractionXml implementation of interactionclassXmlBasicInteractionComplexWrapperWrapper of basic interactions If we add new modelled participants/remove participants, they will be added/removed from the list of participants of the wrapped interaction.classXmlComplexXml implementation of ModelledInteractionclassXmlInteractionEvidenceXml implementation of InteractionEvidenceclassXmlInteractionEvidenceComplexWrapperXml wrapper for interaction evidences used as complexclassXmlModelledInteractionXml implementation of ModelledInteractionclassXmlModelledInteractionComplexWrapperWrapper for complexes that were loaded as abstract interactionsMethods in psidev.psi.mi.jami.xml.model.extension.xml253 that return types with arguments of type Interaction Modifier and Type Method Description ExtendedPsiXmlParticipant<Interaction,Feature>XmlParticipantWrapper. getWrappedParticipant()getWrappedParticipant. -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.xml254
Classes in psidev.psi.mi.jami.xml.model.extension.xml254 with type parameters of type Interaction Modifier and Type Class Description classAbstractXmlParticipant<I extends Interaction,F extends Feature>Abstract class for XmlParticipantstatic classAbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>classAbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>Abstract class for XML Participant poolClasses in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Interaction Modifier and Type Class Description classAbstractPsiXmlInteraction<T extends Participant>Abstract class for xml interactions implementing ExtendedPsiXmlInteraction interfaceclassAbstractXmlBasicInteractionXml implementation of interactionclassAbstractXmlComplexXml implementation for complexclassAbstractXmlInteraction<T extends Participant>Abstract class for xml interactionsclassAbstractXmlInteractionEvidenceXml implementation of InteractionEvidenceclassAbstractXmlModelledInteractionXml implementation of ModelledInteractionclassDefaultXmlBasicInteractionXml implementation of interactionclassDefaultXmlComplexXml implementation for complexclassDefaultXmlInteractionEvidenceXml implementation of InteractionEvidenceclassDefaultXmlModelledInteractionXml implementation of ModelledInteractionclassXmlBasicInteractionXml implementation of interactionclassXmlBasicInteractionComplexWrapperWrapper of basic interactions If we add new modelled participants/remove participants, they will be added/removed from the list of participants of the wrapped interaction.classXmlComplexXml implementation of ModelledInteractionclassXmlInteractionEvidenceXml implementation of InteractionEvidenceclassXmlInteractionEvidenceComplexWrapperXml wrapper for interaction evidences used as complexclassXmlModelledInteractionXml implementation of ModelledInteractionclassXmlModelledInteractionComplexWrapperWrapper for complexes that were loaded as abstract interactionsMethods in psidev.psi.mi.jami.xml.model.extension.xml254 that return types with arguments of type Interaction Modifier and Type Method Description ExtendedPsiXmlParticipant<Interaction,Feature>XmlParticipantWrapper. getWrappedParticipant()getWrappedParticipant. -
Uses of Interaction in psidev.psi.mi.jami.xml.model.extension.xml300
Classes in psidev.psi.mi.jami.xml.model.extension.xml300 with type parameters of type Interaction Modifier and Type Class Description classAbstractXmlParticipant<I extends Interaction,F extends Feature>Abstract class for XmlParticipantstatic classAbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>classAbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>Abstract class for XML Participant poolSubinterfaces of Interaction in psidev.psi.mi.jami.xml.model.extension.xml300 Modifier and Type Interface Description interfaceExtendedPsiXmlInteractionEvidenceExtended interaction evidence for PSI-XML 2,5 standardsinterfaceExtendedPsiXmlModelledInteractionExtended interaction for PSI-XML 2,5 standardsClasses in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Interaction Modifier and Type Class Description classAbstractPsiXmlInteraction<T extends Participant>Abstract class for xml interactions implementing ExtendedPsiXmlInteraction interfaceclassAbstractXmlBasicInteractionXml implementation of interactionclassAbstractXmlComplexXml implementation for complexclassAbstractXmlInteraction<T extends Participant>Abstract class for xml interactionsclassAbstractXmlInteractionEvidenceXml implementation of InteractionEvidenceclassAbstractXmlModelledInteractionXml implementation of ModelledInteractionclassDefaultXmlBasicInteractionXml implementation of interactionclassDefaultXmlComplexXml implementation for complexclassDefaultXmlInteractionEvidenceXml implementation of InteractionEvidenceclassDefaultXmlModelledInteractionXml implementation of ModelledInteractionclassXmlBasicInteractionXml implementation of interactionclassXmlBasicInteractionComplexWrapperWrapper of basic interactions If we add new modelled participants/remove participants, they will be added/removed from the list of participants of the wrapped interaction.classXmlComplexXml implementation of ModelledInteractionclassXmlInteractionEvidenceXml implementation of InteractionEvidenceclassXmlInteractionEvidenceComplexWrapperXml wrapper for interaction evidences used as complexclassXmlModelledInteractionXml 3.0.0 implementation of ModelledInteractionclassXmlModelledInteractionComplexWrapperWrapper for complexes that were loaded as abstract interactionsMethods in psidev.psi.mi.jami.xml.model.extension.xml300 that return types with arguments of type Interaction Modifier and Type Method Description ExtendedPsiXmlParticipant<Interaction,Feature>XmlParticipantWrapper. getWrappedParticipant()getWrappedParticipant. -
Uses of Interaction in psidev.psi.mi.jami.xml.model.reference.xml253
Classes in psidev.psi.mi.jami.xml.model.reference.xml253 with type parameters of type Interaction Modifier and Type Class Description classAbstractParticipantRef<I extends Interaction,T extends Feature>Abstract participant referenceClasses in psidev.psi.mi.jami.xml.model.reference.xml253 that implement Interaction Modifier and Type Class Description classAbstractComplexRefAbstract class for references to a complex -
Uses of Interaction in psidev.psi.mi.jami.xml.model.reference.xml254
Classes in psidev.psi.mi.jami.xml.model.reference.xml254 with type parameters of type Interaction Modifier and Type Class Description classAbstractParticipantRef<I extends Interaction,T extends Feature>Abstract participant referenceClasses in psidev.psi.mi.jami.xml.model.reference.xml254 that implement Interaction Modifier and Type Class Description classAbstractComplexRefAbstract class for references to a complex -
Uses of Interaction in psidev.psi.mi.jami.xml.model.reference.xml300
Classes in psidev.psi.mi.jami.xml.model.reference.xml300 with type parameters of type Interaction Modifier and Type Class Description classAbstractParticipantRef<I extends Interaction,T extends Feature>Abstract participant referenceClasses in psidev.psi.mi.jami.xml.model.reference.xml300 that implement Interaction Modifier and Type Class Description classAbstractComplexRefAbstract class for references to a complex -
Uses of Interaction in psidev.psi.mi.jami.xml.model.xml253
Classes in psidev.psi.mi.jami.xml.model.xml253 with type parameters of type Interaction Modifier and Type Class Description classAbstractEntry<T extends Interaction>Abstract class for EntryMethods in psidev.psi.mi.jami.xml.model.xml253 that return types with arguments of type Interaction Modifier and Type Method Description List<Interaction>BasicEntry.JAXBInteractionsWrapper. getJAXBInteractions() -
Uses of Interaction in psidev.psi.mi.jami.xml.model.xml254
Classes in psidev.psi.mi.jami.xml.model.xml254 with type parameters of type Interaction Modifier and Type Class Description classAbstractEntry<T extends Interaction>Abstract class for EntryMethods in psidev.psi.mi.jami.xml.model.xml254 that return types with arguments of type Interaction Modifier and Type Method Description List<Interaction>BasicEntry.JAXBInteractionsWrapper. getJAXBInteractions() -
Uses of Interaction in psidev.psi.mi.jami.xml.model.xml30
Classes in psidev.psi.mi.jami.xml.model.xml30 with type parameters of type Interaction Modifier and Type Class Description classAbstractEntry<T extends Interaction>Abstract class for EntryMethods in psidev.psi.mi.jami.xml.model.xml30 that return types with arguments of type Interaction Modifier and Type Method Description List<Interaction>BasicEntry.JAXBInteractionsWrapper. getJAXBInteractions()List<Interaction>Entry.JAXBInteractionsWrapper. getJAXBInteractions()
-