Package psidev.psi.mi.jami.crosslink.listener

Class CsvParserLogger

java.lang.Object

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

psidev.psi.mi.jami.crosslink.listener.CsvParserLogger

All Implemented Interfaces:

CsvParserListener, MIFileParserListener

public class CsvParserLogger
extends MIFileParserLogger
implements CsvParserListener

Logger for CsvParser

Since:

24/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
CsvParserLogger()

Method Summary

Modifier and Type	Method	Description
void	onInvalidProteinIdentifierSyntax(String[] identifiers, int lineNumber, int columnNumber)	Event fired when we don't find protein xrefs with db|uniprotId|name
void	onMismatchBetweenPeptideAndLinkedPositions(List<CsvRange> peptidePositions, List<CsvRange> linkedPositions)	Event fired when the number of peptide positions is greater than one and is not the same as the number of linked positions
void	onMismatchBetweenRangePositionsAndProteins(List<CsvRange> rangePositions, List<CsvProtein> proteins)	Event fired when the number of range positions is superior to 1 and the number of proteins is also superior to 1 but does not match the number of ranges
void	onMissingProtein1Column(int lineNumber)	Event fired when the column Protein1 is missing or empty

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

CsvParserLogger

public CsvParserLogger()

Method Detail

onMismatchBetweenPeptideAndLinkedPositions

public void onMismatchBetweenPeptideAndLinkedPositions(List<CsvRange> peptidePositions,
                                                       List<CsvRange> linkedPositions)

Event fired when the number of peptide positions is greater than one and is not the same as the number of linked positions

Specified by:

onMismatchBetweenPeptideAndLinkedPositions in interface CsvParserListener

Parameters:

peptidePositions - : peptide positions in protein sequence

linkedPositions - : linked feature positions relative to peptide positions

onMismatchBetweenRangePositionsAndProteins

public void onMismatchBetweenRangePositionsAndProteins(List<CsvRange> rangePositions,
                                                       List<CsvProtein> proteins)

Event fired when the number of range positions is superior to 1 and the number of proteins is also superior to 1 but does not match the number of ranges

Specified by:

onMismatchBetweenRangePositionsAndProteins in interface CsvParserListener

Parameters:

rangePositions - : feature ranges

proteins - : proteins

onInvalidProteinIdentifierSyntax

public void onInvalidProteinIdentifierSyntax(String[] identifiers,
                                             int lineNumber,
                                             int columnNumber)

Event fired when we don't find protein xrefs with db|uniprotId|name

Specified by:

onInvalidProteinIdentifierSyntax in interface CsvParserListener

Parameters:

identifiers - : the identifiers

lineNumber - a int.

columnNumber - a int.

onMissingProtein1Column

public void onMissingProtein1Column(int lineNumber)

Event fired when the column Protein1 is missing or empty

Specified by:

onMissingProtein1Column in interface CsvParserListener

Parameters:

lineNumber - : line number