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

Class MitabEvidenceStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

InteractionEvidenceStream<InteractionEvidence>, InteractionStream<InteractionEvidence>, MIDataSource, MIFileDataSource, MIFileParserListener, MitabStreamSource<InteractionEvidence>, MitabParserListener

public class MitabEvidenceStreamSource
extends AbstractMitabStreamSource<InteractionEvidence,ParticipantEvidence,FeatureEvidence>
implements InteractionEvidenceStream<InteractionEvidence>

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

Method Summary

Modifier and Type	Method	Description
protected Iterator<InteractionEvidence>	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

MitabEvidenceStreamSource

public MitabEvidenceStreamSource()

Constructor for MitabEvidenceStreamSource.

MitabEvidenceStreamSource

public MitabEvidenceStreamSource(File file)
                          throws IOException

Constructor for MitabEvidenceStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

MitabEvidenceStreamSource

public MitabEvidenceStreamSource(InputStream input)

Constructor for MitabEvidenceStreamSource.

Parameters:

input - a InputStream object.

MitabEvidenceStreamSource

public MitabEvidenceStreamSource(Reader reader)

Constructor for MitabEvidenceStreamSource.

Parameters:

reader - a Reader object.

Method Detail

initialiseMitabLineParser

protected void initialiseMitabLineParser(Reader reader)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

reader - a Reader object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(File file)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

file - a File object.

initialiseMitabLineParser

protected void initialiseMitabLineParser(InputStream input)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

input - a InputStream object.

createMitabIterator

protected Iterator<InteractionEvidence> createMitabIterator()
                                                     throws MIIOException

createMitabIterator.

Specified by:

createMitabIterator in class AbstractMitabStreamSource<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Returns:

a Iterator object.

Throws:

MIIOException

initialiseMitabLineParser

protected void initialiseMitabLineParser(URL url)

initialiseMitabLineParser.

Specified by:

initialiseMitabLineParser in class AbstractMitabStreamSource<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

url - a URL object.