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

Class CsvBinaryEvidenceStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

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

public class CsvBinaryEvidenceStreamSource
extends AbstractCsvStreamSource<BinaryInteractionEvidence>

CrossLink CVS stream source of binary 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
CsvBinaryEvidenceStreamSource()	Constructor for CsvBinaryEvidenceStreamSource.
CsvBinaryEvidenceStreamSource(File file)	Constructor for CsvBinaryEvidenceStreamSource.
CsvBinaryEvidenceStreamSource(InputStream input)	Constructor for CsvBinaryEvidenceStreamSource.
CsvBinaryEvidenceStreamSource(Reader reader)	Constructor for CsvBinaryEvidenceStreamSource.
CsvBinaryEvidenceStreamSource(URL url)	Constructor for CsvBinaryEvidenceStreamSource.

Method Summary

Modifier and Type	Method	Description
protected AbstractCsvInteractionEvidenceParser<BinaryInteractionEvidence>	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

CsvBinaryEvidenceStreamSource

public CsvBinaryEvidenceStreamSource()

Constructor for CsvBinaryEvidenceStreamSource.

CsvBinaryEvidenceStreamSource

public CsvBinaryEvidenceStreamSource(InputStream input)

Constructor for CsvBinaryEvidenceStreamSource.

Parameters:

input - a InputStream object.

CsvBinaryEvidenceStreamSource

public CsvBinaryEvidenceStreamSource(File file)
                              throws IOException

Constructor for CsvBinaryEvidenceStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

CsvBinaryEvidenceStreamSource

public CsvBinaryEvidenceStreamSource(Reader reader)

Constructor for CsvBinaryEvidenceStreamSource.

Parameters:

reader - a Reader object.

CsvBinaryEvidenceStreamSource

public CsvBinaryEvidenceStreamSource(URL url)

Constructor for CsvBinaryEvidenceStreamSource.

Parameters:

url - a URL object.

Method Detail

instantiateLineParser

protected AbstractCsvInteractionEvidenceParser<BinaryInteractionEvidence> instantiateLineParser()

instantiateLineParser.

Specified by:

instantiateLineParser in class AbstractCsvStreamSource<BinaryInteractionEvidence>

Returns:

a AbstractCsvInteractionEvidenceParser object.