Package psidev.psi.mi.jami.listener.impl

Class MIFileParserLogger

java.lang.Object

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

All Implemented Interfaces:

MIFileParserListener

Direct Known Subclasses:

CsvParserLogger, MitabParserLogger, PsiXmlParserLogger

public class MIFileParserLogger
extends Object
implements MIFileParserListener

Logger for MitabParser

Since:

24/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MIFileParserLogger()

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

Methods inherited from class java.lang.Object

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

Constructor Detail

MIFileParserLogger

public MIFileParserLogger()

Method Detail

onMissingCvTermName

public 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.

Specified by:

onMissingCvTermName in interface MIFileParserListener

Parameters:

term - : cv without name

context - : file context

message - : error message

onInvalidSyntax

public void onInvalidSyntax(FileSourceContext context,
                            Exception e)

Listen to an invalid syntax causing an Exception

Specified by:

onInvalidSyntax in interface MIFileParserListener

Parameters:

context - : file context

e - a Exception object.

onSyntaxWarning

public 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.

Specified by:

onSyntaxWarning in interface MIFileParserListener

Parameters:

context - : file context

message - : warning message

onMissingInteractorName

public 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.

Specified by:

onMissingInteractorName in interface MIFileParserListener

Parameters:

interactor - : interactor without name

context - : file context

onParticipantWithoutInteractor

public 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

Specified by:

onParticipantWithoutInteractor in interface MIFileParserListener

Parameters:

participant - : participant without interactor

context - : file context

onInteractionWithoutParticipants

public 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.

Specified by:

onInteractionWithoutParticipants in interface MIFileParserListener

Parameters:

interaction - : interaction without participants

context - : file context

onInvalidOrganismTaxid

public 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)

Specified by:

onInvalidOrganismTaxid in interface MIFileParserListener

Parameters:

taxid - : invalid taxid

context - : file context

onMissingParameterValue

public void onMissingParameterValue(FileSourceContext context)

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

Specified by:

onMissingParameterValue in interface MIFileParserListener

Parameters:

context - : file context

onMissingParameterType

public void onMissingParameterType(FileSourceContext context)

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

Specified by:

onMissingParameterType in interface MIFileParserListener

Parameters:

context - : file context

onMissingConfidenceValue

public void onMissingConfidenceValue(FileSourceContext context)

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

Specified by:

onMissingConfidenceValue in interface MIFileParserListener

Parameters:

context - : file context

onMissingConfidenceType

public void onMissingConfidenceType(FileSourceContext context)

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

Specified by:

onMissingConfidenceType in interface MIFileParserListener

Parameters:

context - : file context

onMissingChecksumValue

public void onMissingChecksumValue(FileSourceContext context)

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

Specified by:

onMissingChecksumValue in interface MIFileParserListener

Parameters:

context - : file context

onMissingChecksumMethod

public void onMissingChecksumMethod(FileSourceContext context)

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

Specified by:

onMissingChecksumMethod in interface MIFileParserListener

Parameters:

context - : file context

onInvalidPosition

public void onInvalidPosition(String message,
                              FileSourceContext context)

Listen to an event fired when a position is not valid

Specified by:

onInvalidPosition in interface MIFileParserListener

Parameters:

message - : error message

context - : file context

onInvalidRange

public void onInvalidRange(String message,
                           FileSourceContext context)

Listen to an event fired when a range is not valid

Specified by:

onInvalidRange in interface MIFileParserListener

Parameters:

message - : error message

context - : file context

onInvalidStoichiometry

public void onInvalidStoichiometry(String message,
                                   FileSourceContext context)

Listen to an event fired when a stoichiometry is not valid

Specified by:

onInvalidStoichiometry in interface MIFileParserListener

Parameters:

message - : : error message

context - : file context

onXrefWithoutDatabase

public void onXrefWithoutDatabase(FileSourceContext context)

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

Specified by:

onXrefWithoutDatabase in interface MIFileParserListener

Parameters:

context - : file context

onXrefWithoutId

public void onXrefWithoutId(FileSourceContext context)

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

Specified by:

onXrefWithoutId in interface MIFileParserListener

Parameters:

context - : file context

onAnnotationWithoutTopic

public void onAnnotationWithoutTopic(FileSourceContext context)

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

Specified by:

onAnnotationWithoutTopic in interface MIFileParserListener

Parameters:

context - : file context

onAliasWithoutName

public void onAliasWithoutName(FileSourceContext context)

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

Specified by:

onAliasWithoutName in interface MIFileParserListener

Parameters:

context - : file context