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

Class MitabBinaryEvidenceStreamSource

java.lang.Object

psidev.psi.mi.jami.tab.extension.datasource.AbstractMitabStreamSource<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

psidev.psi.mi.jami.tab.extension.datasource.MitabBinaryEvidenceStreamSource

All Implemented Interfaces:

BinaryInteractionEvidenceStream, InteractionEvidenceStream<BinaryInteractionEvidence>, InteractionStream<BinaryInteractionEvidence>, MIDataSource, MIFileDataSource, MIFileParserListener, MitabStreamSource<BinaryInteractionEvidence>, MitabParserListener

public class MitabBinaryEvidenceStreamSource
extends AbstractMitabStreamSource<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>
implements BinaryInteractionEvidenceStream

A mitab datasource that loads interaction evidences (full experimental details) It only provides an iterator of the interactions

Since:

25/06/13

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
MitabBinaryEvidenceStreamSource()	Constructor for MitabBinaryEvidenceStreamSource.
MitabBinaryEvidenceStreamSource(File file)	Constructor for MitabBinaryEvidenceStreamSource.
MitabBinaryEvidenceStreamSource(InputStream input)	Constructor for MitabBinaryEvidenceStreamSource.
MitabBinaryEvidenceStreamSource(Reader reader)	Constructor for MitabBinaryEvidenceStreamSource.

Method Summary

Modifier and Type	Method	Description
protected Iterator<BinaryInteractionEvidence>	createMitabIterator()	createMitabIterator.
protected void	initialiseMitabLineParser(File file)	initialiseMitabLineParser.
protected void	initialiseMitabLineParser(InputStream input)	initialiseMitabLineParser.
protected void	initialiseMitabLineParser(Reader reader)	initialiseMitabLineParser.
protected void	initialiseMitabLineParser(URL url)	initialiseMitabLineParser.

Methods inherited from class psidev.psi.mi.jami.tab.extension.datasource.AbstractMitabStreamSource

close, getFileParserListener, getInteractionsIterator, getInteractorFactory, getLineParser, initialiseContext, onAliasWithoutDbSource, onAliasWithoutName, onAnnotationWithoutTopic, onEmptyUniqueIdentifiers, onInteractionWithoutParticipants, onInvalidOrganismTaxid, onInvalidPosition, onInvalidRange, onInvalidStoichiometry, onInvalidSyntax, onMissingChecksumMethod, onMissingChecksumValue, onMissingConfidenceType, onMissingConfidenceValue, onMissingCvTermName, onMissingExpansionId, onMissingInteractorIdentifierColumns, onMissingInteractorName, onMissingParameterType, onMissingParameterValue, onParticipantWithoutInteractor, onSeveralCreatedDateFound, onSeveralCvTermsFound, onSeveralFirstAuthorFound, onSeveralHostOrganismFound, onSeveralOrganismFound, onSeveralSourceFound, onSeveralStoichiometryFound, onSeveralUniqueIdentifiers, onSeveralUpdatedDateFound, onSyntaxWarning, onTextFoundInConfidence, onTextFoundInIdentifier, onXrefWithoutDatabase, onXrefWithoutId, reInit, reset, setFileParserListener, setInteractorFactory, setLineParser, setMIFileParserListener, setMitabFileParserListener, setOriginalFile, setOriginalReader, setOriginalStream, setOriginalURL, validateSyntax, validateSyntax

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.datasource.InteractionStream

getInteractionsIterator

Methods inherited from interface psidev.psi.mi.jami.datasource.MIDataSource

close, initialiseContext, reset

Constructor Detail

MitabBinaryEvidenceStreamSource

public MitabBinaryEvidenceStreamSource()

Constructor for MitabBinaryEvidenceStreamSource.

MitabBinaryEvidenceStreamSource

public MitabBinaryEvidenceStreamSource(File file)
                                throws IOException

Constructor for MitabBinaryEvidenceStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

MitabBinaryEvidenceStreamSource

public MitabBinaryEvidenceStreamSource(InputStream input)

Constructor for MitabBinaryEvidenceStreamSource.

Parameters:

input - a InputStream object.

MitabBinaryEvidenceStreamSource

public MitabBinaryEvidenceStreamSource(Reader reader)

Constructor for MitabBinaryEvidenceStreamSource.

Parameters:

reader - a Reader object.

Method Detail

initialiseMitabLineParser

protected void initialiseMitabLineParser(Reader reader)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

reader - a Reader object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(File file)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

file - a File object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(InputStream input)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

input - a InputStream object.

createMitabIterator

protected Iterator<BinaryInteractionEvidence> createMitabIterator()

createMitabIterator.

Specified by:

createMitabIterator in class AbstractMitabStreamSource<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

Returns:

a Iterator object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(URL url)
                                  throws MIIOException

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

url - a URL object.

Throws:

MIIOException