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

Class CsvEvidenceStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

CsvStreamSource<InteractionEvidence>, CsvParserListener, InteractionEvidenceStream<InteractionEvidence>, InteractionStream<InteractionEvidence>, MIDataSource, MIFileDataSource, MIFileParserListener

public class CsvEvidenceStreamSource
extends AbstractCsvStreamSource<InteractionEvidence>

CrossLink CVS stream 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
CsvEvidenceStreamSource()	Constructor for CsvEvidenceStreamSource.
CsvEvidenceStreamSource(File file)	Constructor for CsvEvidenceStreamSource.
CsvEvidenceStreamSource(InputStream input)	Constructor for CsvEvidenceStreamSource.
CsvEvidenceStreamSource(Reader reader)	Constructor for CsvEvidenceStreamSource.
CsvEvidenceStreamSource(URL url)	Constructor for CsvEvidenceStreamSource.

Method Summary

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

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

close, createCsvIterator, getFileParserListener, getInteractionsIterator, getLineParser, 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

CsvEvidenceStreamSource

public CsvEvidenceStreamSource()

Constructor for CsvEvidenceStreamSource.

CsvEvidenceStreamSource

public CsvEvidenceStreamSource(File file)
                        throws IOException

Constructor for CsvEvidenceStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

CsvEvidenceStreamSource

public CsvEvidenceStreamSource(InputStream input)

Constructor for CsvEvidenceStreamSource.

Parameters:

input - a InputStream object.

CsvEvidenceStreamSource

public CsvEvidenceStreamSource(URL url)

Constructor for CsvEvidenceStreamSource.

Parameters:

url - a URL object.

CsvEvidenceStreamSource

public CsvEvidenceStreamSource(Reader reader)

Constructor for CsvEvidenceStreamSource.

Parameters:

reader - a Reader object.

Method Detail

instantiateLineParser

protected AbstractCsvInteractionEvidenceParser<InteractionEvidence> instantiateLineParser()

instantiateLineParser.

Specified by:

instantiateLineParser in class AbstractCsvStreamSource<InteractionEvidence>

Returns:

a AbstractCsvInteractionEvidenceParser object.