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

Class CsvBinaryEvidenceSource

java.lang.Object

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

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

All Implemented Interfaces:

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

public class CsvBinaryEvidenceSource
extends AbstractCsvSource<BinaryInteractionEvidence>

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

Method Summary

Modifier and Type	Method	Description
protected AbstractCsvInteractionEvidenceParser<BinaryInteractionEvidence>	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

CsvBinaryEvidenceSource

public CsvBinaryEvidenceSource()

Constructor for CsvBinaryEvidenceSource.

CsvBinaryEvidenceSource

public CsvBinaryEvidenceSource(File file)
                        throws IOException

Constructor for CsvBinaryEvidenceSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

CsvBinaryEvidenceSource

public CsvBinaryEvidenceSource(InputStream input)

Constructor for CsvBinaryEvidenceSource.

Parameters:

input - a InputStream object.

CsvBinaryEvidenceSource

public CsvBinaryEvidenceSource(Reader reader)

Constructor for CsvBinaryEvidenceSource.

Parameters:

reader - a Reader object.

CsvBinaryEvidenceSource

public CsvBinaryEvidenceSource(URL url)

Constructor for CsvBinaryEvidenceSource.

Parameters:

url - a URL object.

Method Detail

instantiateLineParser

protected AbstractCsvInteractionEvidenceParser<BinaryInteractionEvidence> instantiateLineParser()

instantiateLineParser.

Specified by:

instantiateLineParser in class AbstractCsvSource<BinaryInteractionEvidence>

Returns:

a AbstractCsvInteractionEvidenceParser object.