Package psidev.psi.mi.jami.crosslink.extension.datasource

Class CsvEvidenceSource

java.lang.Object

psidev.psi.mi.jami.crosslink.extension.datasource.AbstractCsvSource<InteractionEvidence>

psidev.psi.mi.jami.crosslink.extension.datasource.CsvEvidenceSource

All Implemented Interfaces:

CsvSource<InteractionEvidence>, CsvStreamSource<InteractionEvidence>, CsvParserListener, InteractionEvidenceSource<InteractionEvidence>, InteractionEvidenceStream<InteractionEvidence>, InteractionSource<InteractionEvidence>, InteractionStream<InteractionEvidence>, MIDataSource, MIFileDataSource, MIFileParserListener

public class CsvEvidenceSource
extends AbstractCsvSource<InteractionEvidence>

CrossLink CVS source of interaction evidences

Since:

26/08/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.datasource.MIFileDataSource

FILE_URI_PREFIX, URL_PREFIX_REGEXP

Constructor Summary

Constructors

Constructor	Description
CsvEvidenceSource()	Constructor for CsvEvidenceSource.
CsvEvidenceSource(File file)	Constructor for CsvEvidenceSource.
CsvEvidenceSource(InputStream input)	Constructor for CsvEvidenceSource.
CsvEvidenceSource(Reader reader)	Constructor for CsvEvidenceSource.
CsvEvidenceSource(URL url)	Constructor for CsvEvidenceSource.

Method Summary

Modifier and Type	Method	Description
protected AbstractCsvInteractionEvidenceParser<InteractionEvidence>	instantiateLineParser()	instantiateLineParser.

Methods inherited from class psidev.psi.mi.jami.crosslink.extension.datasource.AbstractCsvSource

close, createCsvIterator, getFileParserListener, getInteractions, getInteractionsIterator, getLineParser, getNumberOfInteractions, initialiseContext, onAliasWithoutName, onAnnotationWithoutTopic, onInteractionWithoutParticipants, onInvalidOrganismTaxid, onInvalidPosition, onInvalidProteinIdentifierSyntax, onInvalidRange, onInvalidStoichiometry, onInvalidSyntax, onMismatchBetweenPeptideAndLinkedPositions, onMismatchBetweenRangePositionsAndProteins, onMissingChecksumMethod, onMissingChecksumValue, onMissingConfidenceType, onMissingConfidenceValue, onMissingCvTermName, onMissingInteractorName, onMissingParameterType, onMissingParameterValue, onMissingProtein1Column, onParticipantWithoutInteractor, onSyntaxWarning, onXrefWithoutDatabase, onXrefWithoutId, reInit, reset, setCsvFileParserListener, setFileParserListener, setLineParser, setMIFileParserListener, setOriginalFile, setOriginalReader, setOriginalStream, setOriginalURL, validateSyntax, validateSyntax

Methods inherited from class java.lang.Object

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

Constructor Detail

CsvEvidenceSource

public CsvEvidenceSource()

Constructor for CsvEvidenceSource.

CsvEvidenceSource

public CsvEvidenceSource(File file)
                  throws IOException

Constructor for CsvEvidenceSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

CsvEvidenceSource

public CsvEvidenceSource(InputStream input)

Constructor for CsvEvidenceSource.

Parameters:

input - a InputStream object.

CsvEvidenceSource

public CsvEvidenceSource(Reader reader)

Constructor for CsvEvidenceSource.

Parameters:

reader - a Reader object.

CsvEvidenceSource

public CsvEvidenceSource(URL url)

Constructor for CsvEvidenceSource.

Parameters:

url - a URL object.

Method Detail

instantiateLineParser

protected AbstractCsvInteractionEvidenceParser<InteractionEvidence> instantiateLineParser()

instantiateLineParser.

Specified by:

instantiateLineParser in class AbstractCsvSource<InteractionEvidence>

Returns:

a AbstractCsvInteractionEvidenceParser object.