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

Interface CsvParserListener

All Superinterfaces:

MIFileParserListener

All Known Subinterfaces:

CsvSource<I>, CsvStreamSource<I>

All Known Implementing Classes:

AbstractCsvSource, AbstractCsvStreamSource, CsvBinaryEvidenceSource, CsvBinaryEvidenceStreamSource, CsvEvidenceSource, CsvEvidenceStreamSource, CsvMixedEvidenceSource, CsvNaryEvidenceSource, CsvParserLogger

public interface CsvParserListener
extends MIFileParserListener

A listener listening to events when parsing a crosslink CSV file

Since:

14/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

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 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

onMismatchBetweenPeptideAndLinkedPositions

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

Parameters:

peptidePositions - : peptide positions in protein sequence

linkedPositions - : linked feature positions relative to peptide positions

onMismatchBetweenRangePositionsAndProteins

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

Parameters:

rangePositions - : feature ranges

proteins - : proteins

onInvalidProteinIdentifierSyntax

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

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

Parameters:

identifiers - : the identifiers

lineNumber - a int.

columnNumber - a int.

onMissingProtein1Column

void onMissingProtein1Column(int lineNumber)

Event fired when the column Protein1 is missing or empty

Parameters:

lineNumber - : line number