Package psidev.psi.mi.jami.listener

Interface MIFileParserListener

All Known Subinterfaces:

CsvParserListener, CsvSource<I>, CsvStreamSource<I>, MitabParserListener, MitabSource<I>, MitabStreamSource<I>, PsiXmlParserListener, PsiXmlSource<I>, PsiXmlStreamSource<I>

All Known Implementing Classes:

AbstractCsvSource, AbstractCsvStreamSource, AbstractMitabSource, AbstractMitabStreamSource, AbstractPsiXmlBinarySource, AbstractPsiXmlBinaryStream, AbstractPsiXmlSource, AbstractPsiXmlStream, CsvBinaryEvidenceSource, CsvBinaryEvidenceStreamSource, CsvEvidenceSource, CsvEvidenceStreamSource, CsvMixedEvidenceSource, CsvNaryEvidenceSource, CsvParserLogger, DefaultMitabSource, DefaultMitabStreamSource, DefaultPsiXmlSource, DefaultPsiXmlStreamSource, LightMitabBinarySource, LightMitabBinaryStreamSource, LightMitabSource, LightMitabStreamSource, LightXmlBinarySource, LightXmlBinaryStreamSource, LightXmlSource, LightXmlStreamSource, MIFileParserCompositeListener, MIFileParserLogger, MitabBinaryEvidenceSource, MitabBinaryEvidenceStreamSource, MitabEvidenceSource, MitabEvidenceStreamSource, MitabModelledBinarySource, MitabModelledBinaryStreamSource, MitabModelledSource, MitabModelledStreamSource, MitabParserCompositeListener, MitabParserLogger, PsiXmlParserCompositeListener, PsiXmlParserLogger, XmlBinaryEvidenceSource, XmlBinaryEvidenceStreamSource, XmlBinarySource, XmlBinaryStreamSource, XmlComplexSource, XmlComplexStreamSource, XmlEvidenceSource, XmlEvidenceStreamSource, XmlModelledBinarySource, XmlModelledBinaryStreamSource, XmlModelledSource, XmlModelledStreamSource, XmlSource, XmlStreamSource

public interface MIFileParserListener

Interface for listening to the parsing of a MI file.

Since:

27/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Method Summary

Modifier and Type	Method	Description
void	onAliasWithoutName(FileSourceContext context)	Listen to an event fired when an alias does not have a name
void	onAnnotationWithoutTopic(FileSourceContext context)	Listen to an event fired when an annotation does not have a topic
void	onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)	Listen to an event fired when an interaction is read and does not have any participants.
void	onInvalidOrganismTaxid(String taxid, FileSourceContext context)	Listen to an event fired when an organism does not have a valid taxid (positive integer or -1, -2, -3, -4, -5)
void	onInvalidPosition(String message, FileSourceContext context)	Listen to an event fired when a position is not valid
void	onInvalidRange(String message, FileSourceContext context)	Listen to an event fired when a range is not valid
void	onInvalidStoichiometry(String message, FileSourceContext context)	Listen to an event fired when a stoichiometry is not valid
void	onInvalidSyntax(FileSourceContext context, Exception e)	Listen to an invalid syntax causing an Exception
void	onMissingChecksumMethod(FileSourceContext context)	Listen to an event fired when a checksum does not have a method
void	onMissingChecksumValue(FileSourceContext context)	Listen to an event fired when a checksum does not have a value
void	onMissingConfidenceType(FileSourceContext context)	Listen to an event fired when a confidence does not have a confidence type
void	onMissingConfidenceValue(FileSourceContext context)	Listen to an event fired when a confidence does not have a value
void	onMissingCvTermName(CvTerm term, FileSourceContext context, String message)	Listen to an event fired when a CvTerm is read and does not have any names.
void	onMissingInteractorName(Interactor interactor, FileSourceContext context)	Listen to an event fired when an interactor is read and does not have any names.
void	onMissingParameterType(FileSourceContext context)	Listen to an event fired when a parameter does not have a type
void	onMissingParameterValue(FileSourceContext context)	Listen to an event fired when a parameter does not have a value
void	onParticipantWithoutInteractor(Participant participant, FileSourceContext context)	Listen to en event fired when a Participant is read and no interactor details has been provided.
void	onSyntaxWarning(FileSourceContext context, String message)	Listen to an event fired when the syntax of the file is valid but the content is not expected or some information may be lost.
void	onXrefWithoutDatabase(FileSourceContext context)	Listen to an event fired when a xref does not have a database
void	onXrefWithoutId(FileSourceContext context)	Listen to an event fired when a xref does not have an id

Method Detail

onInvalidSyntax

void onInvalidSyntax(FileSourceContext context,
                     Exception e)

Listen to an invalid syntax causing an Exception

Parameters:

context - : file context

e - a Exception object.

onSyntaxWarning

void onSyntaxWarning(FileSourceContext context,
                     String message)

Listen to an event fired when the syntax of the file is valid but the content is not expected or some information may be lost.

Parameters:

context - : file context

message - : warning message

onMissingCvTermName

void onMissingCvTermName(CvTerm term,
                         FileSourceContext context,
                         String message)

Listen to an event fired when a CvTerm is read and does not have any names. At least a shortname is expected for each CvTerm so such a term may be loaded with an automatically generated shortname.

Parameters:

term - : cv without name

context - : file context

message - : error message

onMissingInteractorName

void onMissingInteractorName(Interactor interactor,
                             FileSourceContext context)

Listen to an event fired when an interactor is read and does not have any names. At least a shortname is expected for each interactor so such an interactor may be loaded with an automatically generated shortname.

Parameters:

interactor - : interactor without name

context - : file context

onParticipantWithoutInteractor

void onParticipantWithoutInteractor(Participant participant,
                                    FileSourceContext context)

Listen to en event fired when a Participant is read and no interactor details has been provided. In such a case, the interactor can be automatically generated as an unknown interactor

Parameters:

participant - : participant without interactor

context - : file context

onInteractionWithoutParticipants

void onInteractionWithoutParticipants(Interaction interaction,
                                      FileSourceContext context)

Listen to an event fired when an interaction is read and does not have any participants. The interaction may be loaded as an empty interaction.

Parameters:

interaction - : interaction without participants

context - : file context

onInvalidOrganismTaxid

void onInvalidOrganismTaxid(String taxid,
                            FileSourceContext context)

Listen to an event fired when an organism does not have a valid taxid (positive integer or -1, -2, -3, -4, -5)

Parameters:

taxid - : invalid taxid

context - : file context

onMissingParameterValue

void onMissingParameterValue(FileSourceContext context)

Listen to an event fired when a parameter does not have a value

Parameters:

context - : file context

onMissingParameterType

void onMissingParameterType(FileSourceContext context)

Listen to an event fired when a parameter does not have a type

Parameters:

context - : file context

onMissingConfidenceValue

void onMissingConfidenceValue(FileSourceContext context)

Listen to an event fired when a confidence does not have a value

Parameters:

context - : file context

onMissingConfidenceType

void onMissingConfidenceType(FileSourceContext context)

Listen to an event fired when a confidence does not have a confidence type

Parameters:

context - : file context

onMissingChecksumValue

void onMissingChecksumValue(FileSourceContext context)

Listen to an event fired when a checksum does not have a value

Parameters:

context - : file context

onMissingChecksumMethod

void onMissingChecksumMethod(FileSourceContext context)

Listen to an event fired when a checksum does not have a method

Parameters:

context - : file context

onInvalidPosition

void onInvalidPosition(String message,
                       FileSourceContext context)

Listen to an event fired when a position is not valid

Parameters:

message - : error message

context - : file context

onInvalidRange

void onInvalidRange(String message,
                    FileSourceContext context)

Listen to an event fired when a range is not valid

Parameters:

message - : error message

context - : file context

onInvalidStoichiometry

void onInvalidStoichiometry(String message,
                            FileSourceContext context)

Listen to an event fired when a stoichiometry is not valid

Parameters:

message - : : error message

context - : file context

onXrefWithoutDatabase

void onXrefWithoutDatabase(FileSourceContext context)

Listen to an event fired when a xref does not have a database

Parameters:

context - : file context

onXrefWithoutId

void onXrefWithoutId(FileSourceContext context)

Listen to an event fired when a xref does not have an id

Parameters:

context - : file context

onAnnotationWithoutTopic

void onAnnotationWithoutTopic(FileSourceContext context)

Listen to an event fired when an annotation does not have a topic

Parameters:

context - : file context

onAliasWithoutName

void onAliasWithoutName(FileSourceContext context)

Listen to an event fired when an alias does not have a name

Parameters:

context - : file context