Package psidev.psi.mi.jami.tab.listener

Interface MitabParserListener

All Superinterfaces:

MIFileParserListener

All Known Subinterfaces:

MitabSource<I>, MitabStreamSource<I>

All Known Implementing Classes:

AbstractMitabSource, AbstractMitabStreamSource, DefaultMitabSource, DefaultMitabStreamSource, LightMitabBinarySource, LightMitabBinaryStreamSource, LightMitabSource, LightMitabStreamSource, MitabBinaryEvidenceSource, MitabBinaryEvidenceStreamSource, MitabEvidenceSource, MitabEvidenceStreamSource, MitabModelledBinarySource, MitabModelledBinaryStreamSource, MitabModelledSource, MitabModelledStreamSource, MitabParserCompositeListener, MitabParserLogger

public interface MitabParserListener
extends MIFileParserListener

A listener listening to events when parsing a mitab file

Since:

14/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Method Summary

Modifier and Type	Method	Description
void	onAliasWithoutDbSource(MitabAlias alias)	onAliasWithoutDbSource.
void	onEmptyUniqueIdentifiers(int line, int column, int mitabColumn)	onEmptyUniqueIdentifiers.
void	onMissingExpansionId(MitabCvTerm expansion)	onMissingExpansionId.
void	onMissingInteractorIdentifierColumns(int line, int column, int mitabColumn)	onMissingInteractorIdentifierColumns.
void	onSeveralCreatedDateFound(Collection<MitabDate> dates)	onSeveralCreatedDateFound.
void	onSeveralCvTermsFound(Collection<MitabCvTerm> terms, FileSourceContext context, String message)	Listen to an event where several CvTerms were found and only one was expected.
void	onSeveralFirstAuthorFound(Collection<MitabAuthor> authors)	onSeveralFirstAuthorFound.
void	onSeveralHostOrganismFound(Collection<MitabOrganism> organisms, FileSourceContext context)	Listen to an event where several host organisms were found in a single experiment and only one was expected.
void	onSeveralOrganismFound(Collection<MitabOrganism> organisms)	onSeveralOrganismFound.
void	onSeveralSourceFound(Collection<MitabSource> sources)	onSeveralSourceFound.
void	onSeveralStoichiometryFound(Collection<MitabStoichiometry> stoichiometry)	onSeveralStoichiometryFound.
void	onSeveralUniqueIdentifiers(Collection<MitabXref> ids)	onSeveralUniqueIdentifiers.
void	onSeveralUpdatedDateFound(Collection<MitabDate> dates)	onSeveralUpdatedDateFound.
void	onTextFoundInConfidence(MitabConfidence conf)	onTextFoundInConfidence.
void	onTextFoundInIdentifier(MitabXref xref)	onTextFoundInIdentifier.

Methods inherited from interface psidev.psi.mi.jami.listener.MIFileParserListener

onAliasWithoutName, onAnnotationWithoutTopic, onInteractionWithoutParticipants, onInvalidOrganismTaxid, onInvalidPosition, onInvalidRange, onInvalidStoichiometry, onInvalidSyntax, onMissingChecksumMethod, onMissingChecksumValue, onMissingConfidenceType, onMissingConfidenceValue, onMissingCvTermName, onMissingInteractorName, onMissingParameterType, onMissingParameterValue, onParticipantWithoutInteractor, onSyntaxWarning, onXrefWithoutDatabase, onXrefWithoutId

Method Detail

onTextFoundInIdentifier

void onTextFoundInIdentifier(MitabXref xref)

onTextFoundInIdentifier.

Parameters:

xref - a MitabXref object.

onTextFoundInConfidence

void onTextFoundInConfidence(MitabConfidence conf)

onTextFoundInConfidence.

Parameters:

conf - a MitabConfidence object.

onMissingExpansionId

void onMissingExpansionId(MitabCvTerm expansion)

onMissingExpansionId.

Parameters:

expansion - a MitabCvTerm object.

onSeveralUniqueIdentifiers

void onSeveralUniqueIdentifiers(Collection<MitabXref> ids)

onSeveralUniqueIdentifiers.

Parameters:

ids - a Collection object.

onEmptyUniqueIdentifiers

void onEmptyUniqueIdentifiers(int line,
                              int column,
                              int mitabColumn)

onEmptyUniqueIdentifiers.

Parameters:

line - a int.

column - a int.

mitabColumn - a int.

onMissingInteractorIdentifierColumns

void onMissingInteractorIdentifierColumns(int line,
                                          int column,
                                          int mitabColumn)

onMissingInteractorIdentifierColumns.

Parameters:

line - a int.

column - a int.

mitabColumn - a int.

onSeveralOrganismFound

void onSeveralOrganismFound(Collection<MitabOrganism> organisms)

onSeveralOrganismFound.

Parameters:

organisms - a Collection object.

onSeveralStoichiometryFound

void onSeveralStoichiometryFound(Collection<MitabStoichiometry> stoichiometry)

onSeveralStoichiometryFound.

Parameters:

stoichiometry - a Collection object.

onSeveralFirstAuthorFound

void onSeveralFirstAuthorFound(Collection<MitabAuthor> authors)

onSeveralFirstAuthorFound.

Parameters:

authors - a Collection object.

onSeveralSourceFound

void onSeveralSourceFound(Collection<MitabSource> sources)

onSeveralSourceFound.

Parameters:

sources - a Collection object.

onSeveralCreatedDateFound

void onSeveralCreatedDateFound(Collection<MitabDate> dates)

onSeveralCreatedDateFound.

Parameters:

dates - a Collection object.

onSeveralUpdatedDateFound

void onSeveralUpdatedDateFound(Collection<MitabDate> dates)

onSeveralUpdatedDateFound.

Parameters:

dates - a Collection object.

onAliasWithoutDbSource

void onAliasWithoutDbSource(MitabAlias alias)

onAliasWithoutDbSource.

Parameters:

alias - a MitabAlias object.

onSeveralCvTermsFound

void onSeveralCvTermsFound(Collection<MitabCvTerm> terms,
                           FileSourceContext context,
                           String message)

Listen to an event where several CvTerms were found and only one was expected. Can happen when reading a clustered interaction evidence for instance

Parameters:

terms - a Collection object.

context - a FileSourceContext object.

message - a String object.

onSeveralHostOrganismFound

void onSeveralHostOrganismFound(Collection<MitabOrganism> organisms,
                                FileSourceContext context)

Listen to an event where several host organisms were found in a single experiment and only one was expected. Can happen when reading a clustered interaction evidence for instance

Parameters:

organisms - a Collection object.

context - a FileSourceContext object.