Uses of Class
psidev.psi.mi.jami.tab.extension.MitabXref

Packages that use MitabXref

Package	Description
psidev.psi.mi.jami.tab.extension.datasource
psidev.psi.mi.jami.tab.io.parser
psidev.psi.mi.jami.tab.listener
psidev.psi.mi.jami.tab.utils

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

Methods in psidev.psi.mi.jami.tab.extension.datasource with parameters of type MitabXref

Modifier and Type	Method	Description
void	AbstractMitabSource.onTextFoundInIdentifier(MitabXref xref)	onTextFoundInIdentifier.
void	AbstractMitabStreamSource.onTextFoundInIdentifier(MitabXref xref)	onTextFoundInIdentifier.
void	DefaultMitabStreamSource.onTextFoundInIdentifier(MitabXref xref)	onTextFoundInIdentifier.

Method parameters in psidev.psi.mi.jami.tab.extension.datasource with type arguments of type MitabXref

Modifier and Type	Method	Description
void	AbstractMitabSource.onSeveralUniqueIdentifiers(Collection<MitabXref> ids)	onSeveralUniqueIdentifiers.
void	AbstractMitabStreamSource.onSeveralUniqueIdentifiers(Collection<MitabXref> ids)	onSeveralUniqueIdentifiers.
void	DefaultMitabStreamSource.onSeveralUniqueIdentifiers(Collection<MitabXref> ids)	onSeveralUniqueIdentifiers.

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

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

Modifier and Type	Method	Description
MitabXref	MitabLineParser.id(CvTerm qualifier, boolean recognizeImexPrimary, int columnNumber)

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

Modifier and Type	Method	Description
Collection<MitabXref>	MitabLineParser.ids(CvTerm qualifier, boolean recognizeImex, int column)

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

Modifier and Type	Method	Description
protected void	AbstractInteractionLineParser.createAliasFromAltId(Interactor interactor, MitabXref ref)	createAliasFromAltId.
protected void	AbstractInteractionLineParser.createChecksumFromAltId(Interactor interactor, MitabXref ref)	createChecksumFromAltId.
protected void	AbstractInteractionLineParser.createChecksumFromId(Interaction interaction, MitabXref ref)	createChecksumFromId.

Method parameters in psidev.psi.mi.jami.tab.io.parser with type arguments of type MitabXref

Modifier and Type	Method	Description
protected Interactor	AbstractInteractionLineParser.createInteractorFrom(Collection<MitabXref> uniqueId, Collection<MitabXref> altid, Collection<MitabAlias> aliases, Collection<MitabOrganism> taxid, Collection<MitabCvTerm> type, Collection<MitabXref> xref, Collection<MitabChecksum> checksum, int line, int column, int mitabColumn)	createInteractorFrom.
protected void	AbstractInteractionLineParser.fillInteractorWithAlternativeIdentifiers(Collection<MitabXref> altid, Interactor interactor)	fillInteractorWithAlternativeIdentifiers.
protected String[]	AbstractInteractionLineParser.findInteractorShortNameAndFullNameFrom(Collection<MitabXref> uniqueId, Collection<MitabXref> altid, Collection<MitabAlias> aliases, int line, int column, int mitabColumn)	findInteractorShortNameAndFullNameFrom.
protected void	AbstractInteractionLineParser.initialiseInteractionIdentifiers(Collection<MitabXref> interactionIds, T interaction)	initialiseInteractionIdentifiers.
protected boolean	AbstractInteractionEvidenceLineParser.initialisePublicationIdentifiers(Collection<MitabXref> pubId, MitabPublication publication, boolean hasInitialisedLocator)	initialisePublicationIdentifiers.
protected void	AbstractInteractionLineParser.processInteractorPool(Collection<MitabXref> xref, InteractorPool interactor)	processInteractorPool.

Uses of MitabXref in psidev.psi.mi.jami.tab.listener

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

Modifier and Type	Method	Description
void	MitabParserCompositeListener.onTextFoundInIdentifier(MitabXref xref)	onTextFoundInIdentifier.
void	MitabParserListener.onTextFoundInIdentifier(MitabXref xref)	onTextFoundInIdentifier.
void	MitabParserLogger.onTextFoundInIdentifier(MitabXref xref)	onTextFoundInIdentifier.

Method parameters in psidev.psi.mi.jami.tab.listener with type arguments of type MitabXref

Modifier and Type	Method	Description
void	MitabParserCompositeListener.onSeveralUniqueIdentifiers(Collection<MitabXref> ids)	onSeveralUniqueIdentifiers.
void	MitabParserListener.onSeveralUniqueIdentifiers(Collection<MitabXref> ids)	onSeveralUniqueIdentifiers.
void	MitabParserLogger.onSeveralUniqueIdentifiers(Collection<MitabXref> ids)	onSeveralUniqueIdentifiers.

Uses of MitabXref in psidev.psi.mi.jami.tab.utils

Methods in psidev.psi.mi.jami.tab.utils that return MitabXref

Modifier and Type	Method	Description
static MitabXref	MitabUtils.findBestShortNameFromAlternativeIdentifiers(Collection<MitabXref> altids)	Find the best id to use as a shortname.

Method parameters in psidev.psi.mi.jami.tab.utils with type arguments of type MitabXref

Modifier and Type	Method	Description
static MitabXref	MitabUtils.findBestShortNameFromAlternativeIdentifiers(Collection<MitabXref> altids)	Find the best id to use as a shortname.