Uses of Interface
psidev.psi.mi.jami.binary.BinaryInteraction

Packages that use BinaryInteraction

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

Uses of BinaryInteraction in psidev.psi.mi.jami.binary

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

Modifier and Type	Interface	Description
interface	BinaryInteractionEvidence	A BinaryInteractionEvidence is an InteractionEvidence with only two participants
interface	ModelledBinaryInteraction	A ModelledBinary interaction is a ModelledInteraction with only two participants

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

Classes in psidev.psi.mi.jami.binary.expansion with type parameters of type BinaryInteraction

Modifier and Type	Class	Description
class	AbstractBipartiteExpansion<T extends Interaction,B extends BinaryInteraction>	Abstract class for BipartiteExpansion.
class	AbstractComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>	Abstract class for ComplexExpansionMethod.
class	AbstractMatrixExpansion<T extends Interaction,B extends BinaryInteraction>	Abstract class for Matrix expansion
class	AbstractSpokeExpansion<T extends Interaction,B extends BinaryInteraction>	Abstract class for SpokeExpansion
interface	ComplexExpansionMethod<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 that return BinaryInteraction

Modifier and Type	Method	Description
protected BinaryInteraction	BipartiteExpansion.createBinaryInteraction(Interaction interaction, Participant c1, Participant c2)	createBinaryInteraction
protected <P extends Participant> BinaryInteraction	MatrixExpansion.createBinaryInteraction(Interaction interaction, P c1, P c2)	createBinaryInteraction
protected BinaryInteraction	SpokeExpansion.createBinaryInteraction(Interaction interaction, Participant c1, Participant c2)	createBinaryInteraction

Methods in psidev.psi.mi.jami.binary.expansion that return types with arguments of type BinaryInteraction

Modifier and Type	Method	Description
Collection<BinaryInteraction>	BipartiteExpansion.expand(Interaction interaction)	expand
Collection<BinaryInteraction>	MatrixExpansion.expand(Interaction interaction)	expand
Collection<BinaryInteraction>	SpokeExpansion.expand(Interaction interaction)	expand

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

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

Modifier and Type	Class	Description
class	AbstractBinaryInteraction<T extends Participant>	Abstract class for BinaryInteraction.
class	AbstractBinaryInteractionWrapper<I extends Interaction<T>,T extends Participant>	Abstract class for binary interactions that wrap an Interaction.
class	BinaryInteractionEvidenceWrapper	A wrapper for InteractionEvidence which contains two participants
class	BinaryInteractionWrapper	Binary Wrapper for an Interaction
class	DefaultBinaryInteraction	Default implementation for BinaryInteraction Note: the methods equals and hashCode have not been overridden.
class	DefaultBinaryInteractionEvidence	Default implementation for BinaryInteractionEvidence
class	DefaultModelledBinaryInteraction	Default implementation for ModelledBinaryInteraction
class	DefaultNamedBinaryInteraction	Default implementation of a named binary interaction
class	DefaultNamedBinaryInteractionEvidence	Default implementation of a Named binary interaction evidence
class	DefaultNamedModelledBinaryInteraction	Default implementation for Named modelled binary interaction
class	ModelledBinaryInteractionWrapper	A wrapper for ModelledInteraction which contains two participants

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

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

Modifier and Type	Class	Description
class	CsvBinaryInteractionEvidence	Crosslink CSV implementation of BinaryInteractionEvidence

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

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

Modifier and Type	Interface	Description
interface	BinaryInteractionSource<T extends BinaryInteraction>	A Data source of binary interactions.
interface	BinaryInteractionStream<T extends BinaryInteraction>	A Data source of binary interactions giving only a stream of interactions.

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

Methods in psidev.psi.mi.jami.factory that return BinaryInteraction

Modifier and Type	Method	Description
BinaryInteraction	BinaryInteractionFactory.createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)	Create a new BinaryInteraction object from an Interaction parent and two participants
BinaryInteraction	DefaultBinaryInteractionFactory.createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)	Create a new BinaryInteraction object from an Interaction parent and two participants
BinaryInteraction	BinaryInteractionFactory.createBinaryInteractionWrapperFrom(Interaction interaction)	Creates a BinaryInteraction that wraps the given interaction
BinaryInteraction	DefaultBinaryInteractionFactory.createBinaryInteractionWrapperFrom(Interaction interaction)	Creates a BinaryInteraction that wraps the given interaction
BinaryInteraction	BinaryInteractionFactory.createSelfBinaryInteractionFrom(Interaction interaction)	Create a binary interaction representing a self interaction
BinaryInteraction	DefaultBinaryInteractionFactory.createSelfBinaryInteractionFrom(Interaction interaction)	Create a binary interaction representing a self interaction
BinaryInteraction	BinaryInteractionFactory.instantiateNewBinaryInteraction()	Instantiate a new BinaryInteraction
BinaryInteraction	DefaultBinaryInteractionFactory.instantiateNewBinaryInteraction()	instantiateNewBinaryInteraction

Methods in psidev.psi.mi.jami.factory that return types with arguments of type BinaryInteraction

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)

Uses of BinaryInteraction in psidev.psi.mi.jami.json

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

Modifier and Type	Method	Description
static String[]	MIJsonUtils.extractBinaryInteractionId(Xref ref, BinaryInteraction interaction, Integer number)	extractBinaryInteractionId.

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

Classes in psidev.psi.mi.jami.json.binary with type parameters of type BinaryInteraction

Modifier and Type	Class	Description
class	AbstractMIJsonBinaryWriter<I extends BinaryInteraction>	Abstract JSON writer for binary interactions (binary json format)
class	AbstractMIJsonWriter<I extends Interaction,B extends BinaryInteraction>	The jsonWriter which writes the interactions

Methods in psidev.psi.mi.jami.json.binary with parameters of type BinaryInteraction

Modifier and Type	Method	Description
void	MIJsonBinaryWriter.write(BinaryInteraction interaction)	write.

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

Constructor	Description
LightMIJsonWriter(File file, OntologyTermFetcher fetcher, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMIJsonWriter.
LightMIJsonWriter(OutputStream output, OntologyTermFetcher fetcher, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMIJsonWriter.
LightMIJsonWriter(Writer writer, OntologyTermFetcher fetcher, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMIJsonWriter.
MIJsonWriter(File file, OntologyTermFetcher fetcher, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for MIJsonWriter.
MIJsonWriter(OutputStream output, OntologyTermFetcher fetcher, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for MIJsonWriter.
MIJsonWriter(Writer writer, OntologyTermFetcher fetcher, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for MIJsonWriter.

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

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

Modifier and Type	Class	Description
class	SimpleJsonBinaryInteractionWriter<I extends BinaryInteraction>	Json writer for interactions

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

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

Modifier and Type	Class	Description
class	MitabBinaryInteraction	A MitabBinaryInteraction is a binaryInteraction with a MitabSourceLocator
class	MitabBinaryInteractionEvidence	TODO comment this
class	MitabModelledBinaryInteraction	A MitabBinaryInteraction is a modelled binaryInteraction with a MitabSourceLocator

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

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

Modifier and Type	Method	Description
protected Iterator<BinaryInteraction>	LightMitabBinaryStreamSource.createMitabIterator()	createMitabIterator.

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

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

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

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

Methods in psidev.psi.mi.jami.tab.io.parser with parameters of type BinaryInteraction

Modifier and Type	Method	Description
protected void	BinaryLineParser.addParticipant(Participant participant, BinaryInteraction interaction)	addParticipant.
protected void	BinaryLineParser.initialiseExpansionMethod(Collection<MitabCvTerm> expansion, BinaryInteraction interaction)	initialiseExpansionMethod.

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

Classes in psidev.psi.mi.jami.tab.io.writer with type parameters of type BinaryInteraction

Modifier and Type	Class	Description
class	AbstractMitab25BinaryWriter<T extends BinaryInteraction,P extends Participant>	Abstract class for BinaryInteraction writer.
class	AbstractMitab26BinaryWriter<T extends BinaryInteraction,P extends Participant>	Abstract class for MITAB 2.6 writer of binary interactions
class	AbstractMitab27BinaryWriter<T extends BinaryInteraction,P extends Participant>	Abstract mitab 2.7 writer for binary interactions
class	AbstractMitab28BinaryWriter<T extends BinaryInteraction,P extends Participant>	Abstract mitab 2.8 writer for binary interactions
class	AbstractMitabWriter<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 BinaryInteraction

Modifier and Type	Method	Description
void	Mitab25BinaryWriter.write(BinaryInteraction interaction)	Writes a binary interaction.
void	Mitab26BinaryWriter.write(BinaryInteraction interaction)	Writes a binary interaction.
void	Mitab27BinaryWriter.write(BinaryInteraction interaction)	Writes a binary interaction.
void	Mitab28BinaryWriter.write(BinaryInteraction interaction)	Writes a binary interaction.

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

Modifier and Type	Method	Description
protected void	LightMitab25Writer.initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	Mitab25Writer.initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	initialiseExpansionMethod.

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

Constructor	Description
LightMitab25Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab25Writer.
LightMitab25Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab25Writer.
LightMitab25Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab25Writer.
LightMitab26Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab26Writer.
LightMitab26Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab26Writer.
LightMitab26Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab26Writer.
LightMitab27Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab27Writer.
LightMitab27Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab27Writer.
LightMitab27Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab27Writer.
LightMitab28Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab28Writer.
LightMitab28Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab28Writer.
LightMitab28Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for LightMitab28Writer.
Mitab25Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab25Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab25Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab26Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab26Writer.
Mitab26Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab26Writer.
Mitab26Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab26Writer.
Mitab27Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab27Writer.
Mitab27Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab27Writer.
Mitab27Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab27Writer.
Mitab28Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab28Writer.
Mitab28Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab28Writer.
Mitab28Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab28Writer.

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

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

Modifier and Type	Method	Description
protected void	Mitab25Writer.initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	initialiseExpansionMethod.

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

Constructor	Description
Mitab25Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab25Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab25Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab26Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab26Writer.
Mitab26Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab26Writer.
Mitab26Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab26Writer.
Mitab27Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab27Writer.
Mitab27Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab27Writer.
Mitab27Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab27Writer.
Mitab28Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab28Writer.
Mitab28Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab28Writer.
Mitab28Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab28Writer.

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

Classes in psidev.psi.mi.jami.tab.io.writer.feeder with type parameters of type BinaryInteraction

Modifier and Type	Class	Description
class	AbstractMitabColumnFeeder<T extends BinaryInteraction,P extends Participant>	Abstract Mitab 2.5 column feeder
interface	MitabColumnFeeder<T extends BinaryInteraction,P extends Participant>	A MITAB 2.5 column feeder will write the content of MITAB 2.5 columns

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

Modifier and Type	Method	Description
void	DefaultMitabColumnFeeder.writeFirstAuthor(BinaryInteraction interaction)	Writes the first author of a publication in an experiment
void	DefaultMitabColumnFeeder.writeHostOrganism(BinaryInteraction interaction)	Writes experiment host organism
void	DefaultMitabColumnFeeder.writeInteractionAnnotations(BinaryInteraction interaction)	Writes interaction annotations
void	DefaultMitabColumnFeeder.writeInteractionConfidences(BinaryInteraction interaction)	Writes the confidences of an interaction evidence
void	DefaultMitabColumnFeeder.writeInteractionDetectionMethod(BinaryInteraction interaction)	Writes the interaction detection method of the experiment.
void	DefaultMitabColumnFeeder.writeInteractionIdentifiers(BinaryInteraction interaction)	Writes the interaction identifiers of an interaction.
void	DefaultMitabColumnFeeder.writeInteractionParameters(BinaryInteraction interaction)	Writes interaction parameters
void	DefaultMitabColumnFeeder.writeInteractionXrefs(BinaryInteraction interaction)	Write interaction Xref r
void	DefaultMitabColumnFeeder.writeNegativeProperty(BinaryInteraction interaction)	Writes interaction negative property if true
void	DefaultMitabColumnFeeder.writePublicationIdentifiers(BinaryInteraction interaction)	Writes the publication identifiers of a publication in an experiment.
void	DefaultMitabColumnFeeder.writeSource(BinaryInteraction interaction)	Writes the interaction source from the modelled interaction

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

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

Modifier and Type	Method	Description
static BinaryInteraction	InteractionUtils.createBinaryInteractionFrom(Interaction interaction)	Create a BinaryInteractionWrapper from the given interaction which should contain not more than two participants.
static BinaryInteraction	InteractionUtils.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.

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

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

Modifier and Type	Method	Description
static void	InteractionCloner.copyAndOverrideBasicParticipantsToBinary(Interaction source, BinaryInteraction target, boolean createNewParticipant, boolean self)	This method will copy participants of interaction source in binary target.

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

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

Constructor	Description
XmlBinaryInteractionIterator(PsiXmlParser<BinaryInteraction> lineParser)	Constructor for XmlBinaryInteractionIterator.

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

Classes in psidev.psi.mi.jami.xml.io.parser with type parameters of type BinaryInteraction

Modifier and Type	Class	Description
class	AbstractPsixmlBinaryParser<T extends Interaction,B extends BinaryInteraction>	Abstract class for a binary interaction parser

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

Modifier and Type	Method	Description
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 BinaryInteraction in psidev.psi.mi.jami.xml.io.writer.compact

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

Modifier and Type	Method	Description
protected void	LightCompactXmlBinaryWriter.registerAvailabilities(BinaryInteraction interaction)	registerAvailabilities.
protected void	LightCompactXmlNamedBinaryWriter.registerAvailabilities(BinaryInteraction interaction)	registerAvailabilities.
protected void	LightCompactXmlBinaryWriter.registerExperiment(BinaryInteraction interaction)	registerExperiment.
protected void	LightCompactXmlNamedBinaryWriter.registerExperiment(BinaryInteraction interaction)	registerExperiment.

Uses of BinaryInteraction 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 BinaryInteraction

Modifier and Type	Method	Description
protected void	LightCompactXmlBinaryWriter.registerAvailabilities(BinaryInteraction interaction)	registerAvailabilities.
protected void	LightCompactXmlBinaryWriter.registerExperiment(BinaryInteraction interaction)	registerExperiment.

Uses of BinaryInteraction 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 BinaryInteraction

Modifier and Type	Method	Description
protected void	XmlBasicBinaryInteractionWriter.writeAttributes(BinaryInteraction object)	writeAttributes.
protected CvTerm	XmlBasicBinaryInteractionWriter.writeExperiments(BinaryInteraction object)	writeExperiments.
protected void	XmlNamedBinaryInteractionWriter.writeNames(BinaryInteraction object)	writeNames.

Uses of BinaryInteraction 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 BinaryInteraction

Modifier and Type	Method	Description
protected void	XmlBasicBinaryInteractionWriter.writeAttributes(BinaryInteraction object)	writeAttributes.
protected CvTerm	XmlBasicBinaryInteractionWriter.writeExperiments(BinaryInteraction object)	writeExperiments.
protected void	XmlNamedBinaryInteractionWriter.writeNames(BinaryInteraction object)	writeNames.

Uses of BinaryInteraction 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 BinaryInteraction

Modifier and Type	Method	Description
protected void	XmlBasicBinaryInteractionWriter.writeAttributes(BinaryInteraction object)	writeAttributes.
protected CvTerm	XmlBasicBinaryInteractionWriter.writeExperiments(BinaryInteraction object)	writeExperiments.

Uses of BinaryInteraction 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 BinaryInteraction

Modifier and Type	Method	Description
protected void	XmlBasicBinaryInteractionWriter.writeAttributes(BinaryInteraction object)	writeAttributes.
protected CvTerm	XmlBasicBinaryInteractionWriter.writeExperiments(BinaryInteraction object)	writeExperiments.

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

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

Modifier and Type	Class	Description
class	AbstractExtendedXmlBinaryInteraction<P extends Participant>	Abstract class for xml binary interactions
class	AbstractXmlBinaryInteraction<P extends Participant>	Abstract class for xml binary interactions
class	AbstractXmlBinaryInteractionEvidence	Abstract class for Xml BinaryInteractionEvidence
class	XmlBinaryInteraction	Xml implementation of binary interaction
class	XmlBinaryInteractionEvidenceWrapper	Xml implementation of BinaryInteractionWrapper with a source locator
class	XmlBinaryInteractionWrapper	Wrapper for ModelledBinaryInteraction
class	XmlModelledBinaryInteraction	Xml implementation of ModelledInteraction
class	XmlModelledBinaryInteractionWrapper	Wrapper for Xml binary interactions

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

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

Modifier and Type	Class	Description
class	XmlBinaryInteractionEvidence	Xml implementation of BinaryInteractionEvidence

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

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

Modifier and Type	Class	Description
class	XmlBinaryInteractionEvidence	Xml implementation of BinaryInteractionEvidence

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

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

Modifier and Type	Class	Description
class	XmlBinaryInteractionEvidence	Xml implementation of BinaryInteractionEvidence
class	XmlBinaryInteractionEvidenceWrapper	Xml implementation of BinaryInteractionWrapper with a source locator
class	XmlModelledBinaryInteraction	Xml implementation of ModelledInteraction
class	XmlModelledBinaryInteractionWrapper	Wrapper for Xml binary interactions

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

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

Modifier and Type	Class	Description
class	AbstractPsiXmlBinarySource<T extends Interaction,B extends BinaryInteraction>	Abstract class for Psi-XML binary interaction data source which loads the full interaction dataset
class	AbstractPsiXmlBinaryStream<T extends Interaction,B extends BinaryInteraction>	Abstract class for binary interaction datasources

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

Modifier and Type	Method	Description
protected Iterator<BinaryInteraction>	LightXmlBinaryStreamSource.createXmlIterator()	createXmlIterator.
protected Iterator<BinaryInteraction>	XmlBinaryStreamSource.createXmlIterator()	createXmlIterator.

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

Modifier and Type	Method	Description
protected void	AbstractPsiXmlBinarySource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	AbstractPsiXmlBinaryStream.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected abstract void	AbstractPsiXmlStream.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	LightXmlSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	LightXmlStreamSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlComplexSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlComplexStreamSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlEvidenceSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlEvidenceStreamSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlModelledSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlModelledStreamSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	XmlStreamSource.initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.

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

Methods in psidev.psi.mi.jami.xml.model.extension.factory.xml25 that return BinaryInteraction

Modifier and Type	Method	Description
BinaryInteraction	XmlBinaryInteractionFactory.createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)	Create a new BinaryInteraction object from an Interaction parent and two participants
BinaryInteraction	XmlBinaryInteractionFactory.createBinaryInteractionWrapperFrom(Interaction interaction)	Creates a BinaryInteraction that wraps the given interaction
BinaryInteraction	XmlBinaryInteractionFactory.createSelfBinaryInteractionFrom(Interaction interaction)	Create a binary interaction representing a self interaction

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

Methods in psidev.psi.mi.jami.xml.model.extension.factory.xml30 that return BinaryInteraction

Modifier and Type	Method	Description
BinaryInteraction	XmlBinaryInteractionFactory.createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)	Create a new BinaryInteraction object from an Interaction parent and two participants
BinaryInteraction	XmlBinaryInteractionFactory.createBinaryInteractionWrapperFrom(Interaction interaction)	Creates a BinaryInteraction that wraps the given interaction
BinaryInteraction	XmlBinaryInteractionFactory.createSelfBinaryInteractionFrom(Interaction interaction)	Create a binary interaction representing a self interaction
BinaryInteraction	XmlBinaryInteractionFactory.instantiateNewBinaryInteraction()	Instantiate a new BinaryInteraction