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

Class MitabParserLogger

java.lang.Object

psidev.psi.mi.jami.listener.impl.MIFileParserLogger

psidev.psi.mi.jami.tab.listener.MitabParserLogger

All Implemented Interfaces:

MIFileParserListener, MitabParserListener

public class MitabParserLogger
extends MIFileParserLogger
implements MitabParserListener

Logger for MitabParser

Since:

24/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MitabParserLogger()

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 class psidev.psi.mi.jami.listener.impl.MIFileParserLogger

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

Constructor Detail

MitabParserLogger

public MitabParserLogger()

Method Detail

onTextFoundInIdentifier

public void onTextFoundInIdentifier(MitabXref xref)

onTextFoundInIdentifier.

Specified by:

onTextFoundInIdentifier in interface MitabParserListener

Parameters:

xref - a MitabXref object.

onTextFoundInConfidence

public void onTextFoundInConfidence(MitabConfidence conf)

onTextFoundInConfidence.

Specified by:

onTextFoundInConfidence in interface MitabParserListener

Parameters:

conf - a MitabConfidence object.

onMissingExpansionId

public void onMissingExpansionId(MitabCvTerm expansion)

onMissingExpansionId.

Specified by:

onMissingExpansionId in interface MitabParserListener

Parameters:

expansion - a MitabCvTerm object.

onSeveralUniqueIdentifiers

public void onSeveralUniqueIdentifiers(Collection<MitabXref> ids)

onSeveralUniqueIdentifiers.

Specified by:

onSeveralUniqueIdentifiers in interface MitabParserListener

Parameters:

ids - a Collection object.

onEmptyUniqueIdentifiers

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

onEmptyUniqueIdentifiers.

Specified by:

onEmptyUniqueIdentifiers in interface MitabParserListener

Parameters:

line - a int.

column - a int.

mitabColumn - a int.

onSeveralCvTermsFound

public 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

Specified by:

onSeveralCvTermsFound in interface MitabParserListener

Parameters:

terms - a Collection object.

context - a FileSourceContext object.

message - a String object.

onMissingInteractorIdentifierColumns

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

onMissingInteractorIdentifierColumns.

Specified by:

onMissingInteractorIdentifierColumns in interface MitabParserListener

Parameters:

line - a int.

column - a int.

mitabColumn - a int.

onSeveralOrganismFound

public void onSeveralOrganismFound(Collection<MitabOrganism> organisms)

onSeveralOrganismFound.

Specified by:

onSeveralOrganismFound in interface MitabParserListener

Parameters:

organisms - a Collection object.

onSeveralStoichiometryFound

public void onSeveralStoichiometryFound(Collection<MitabStoichiometry> stoichiometry)

onSeveralStoichiometryFound.

Specified by:

onSeveralStoichiometryFound in interface MitabParserListener

Parameters:

stoichiometry - a Collection object.

onSeveralFirstAuthorFound

public void onSeveralFirstAuthorFound(Collection<MitabAuthor> authors)

onSeveralFirstAuthorFound.

Specified by:

onSeveralFirstAuthorFound in interface MitabParserListener

Parameters:

authors - a Collection object.

onSeveralSourceFound

public void onSeveralSourceFound(Collection<MitabSource> sources)

onSeveralSourceFound.

Specified by:

onSeveralSourceFound in interface MitabParserListener

Parameters:

sources - a Collection object.

onSeveralHostOrganismFound

public 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

Specified by:

onSeveralHostOrganismFound in interface MitabParserListener

Parameters:

organisms - a Collection object.

context - a FileSourceContext object.

onSeveralCreatedDateFound

public void onSeveralCreatedDateFound(Collection<MitabDate> dates)

onSeveralCreatedDateFound.

Specified by:

onSeveralCreatedDateFound in interface MitabParserListener

Parameters:

dates - a Collection object.

onSeveralUpdatedDateFound

public void onSeveralUpdatedDateFound(Collection<MitabDate> dates)

onSeveralUpdatedDateFound.

Specified by:

onSeveralUpdatedDateFound in interface MitabParserListener

Parameters:

dates - a Collection object.

onAliasWithoutDbSource

public void onAliasWithoutDbSource(MitabAlias alias)

onAliasWithoutDbSource.

Specified by:

onAliasWithoutDbSource in interface MitabParserListener

Parameters:

alias - a MitabAlias object.