Package psidev.psi.mi.jami.xml.model.extension.datasource

Class XmlEvidenceStreamSource

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.datasource.AbstractPsiXmlStream<InteractionEvidence>

psidev.psi.mi.jami.xml.model.extension.datasource.XmlEvidenceStreamSource

All Implemented Interfaces:

ErrorHandler, InteractionEvidenceStream<InteractionEvidence>, InteractionStream<InteractionEvidence>, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlStreamSource<InteractionEvidence>

public class XmlEvidenceStreamSource
extends AbstractPsiXmlStream<InteractionEvidence>
implements InteractionEvidenceStream<InteractionEvidence>

Datasource for Psi-xml interaction evidence

Since:

17/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.xml.model.extension.datasource.AbstractPsiXmlStream

SCHEMA_FEATURE, VALIDATION_FEATURE

Fields inherited from interface psidev.psi.mi.jami.datasource.MIFileDataSource

FILE_URI_PREFIX, URL_PREFIX_REGEXP

Constructor Summary

Constructors

Constructor	Description
XmlEvidenceStreamSource()	Constructor for XmlEvidenceStreamSource.
XmlEvidenceStreamSource(File file)	Constructor for XmlEvidenceStreamSource.
XmlEvidenceStreamSource(InputStream input)	Constructor for XmlEvidenceStreamSource.
XmlEvidenceStreamSource(Reader reader)	Constructor for XmlEvidenceStreamSource.
XmlEvidenceStreamSource(URL url)	Constructor for XmlEvidenceStreamSource.

Method Summary

Modifier and Type	Method	Description
protected Iterator<InteractionEvidence>	createXmlIterator()	createXmlIterator.
protected void	initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	initialiseXmlParser(File file)	initialiseXmlParser.
protected void	initialiseXmlParser(InputStream input)	initialiseXmlParser.
protected void	initialiseXmlParser(Reader reader)	initialiseXmlParser.
protected void	initialiseXmlParser(URL url)	initialiseXmlParser.

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.datasource.AbstractPsiXmlStream

close, error, fatalError, getElementCache, getFileParserListener, getInteractionsIterator, getInteractorFactory, getParser, initialiseContext, isInitialised, onAliasWithoutName, onAnnotationWithoutTopic, onInteractionWithoutParticipants, onInvalidOrganismTaxid, onInvalidPosition, onInvalidRange, onInvalidStoichiometry, onInvalidSyntax, onMissingChecksumMethod, onMissingChecksumValue, onMissingConfidenceType, onMissingConfidenceValue, onMissingCvTermName, onMissingInteractorName, onMissingParameterType, onMissingParameterValue, onParticipantWithoutInteractor, onSeveralExperimentalRolesFound, onSeveralExperimentsFound, onSeveralExpressedInOrganismFound, onSeveralHostOrganismFound, onSyntaxWarning, onUnresolvedReference, onXrefWithoutDatabase, onXrefWithoutId, reInit, reset, setFileParserListener, setInteractorFactory, setMIFileParserListener, setParser, setXmlFileParserListener, validateSyntax, validateSyntax, warning

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

XmlEvidenceStreamSource

public XmlEvidenceStreamSource()

Constructor for XmlEvidenceStreamSource.

XmlEvidenceStreamSource

public XmlEvidenceStreamSource(File file)

Constructor for XmlEvidenceStreamSource.

Parameters:

file - a File object.

XmlEvidenceStreamSource

public XmlEvidenceStreamSource(InputStream input)

Constructor for XmlEvidenceStreamSource.

Parameters:

input - a InputStream object.

XmlEvidenceStreamSource

public XmlEvidenceStreamSource(Reader reader)

Constructor for XmlEvidenceStreamSource.

Parameters:

reader - a Reader object.

XmlEvidenceStreamSource

public XmlEvidenceStreamSource(URL url)

Constructor for XmlEvidenceStreamSource.

Parameters:

url - a URL object.

Method Detail

initialiseXmlParser

protected void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<InteractionEvidence>

Parameters:

reader - a Reader object.

initialiseXmlParser

protected void initialiseXmlParser(File file)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<InteractionEvidence>

Parameters:

file - a File object.

initialiseXmlParser

protected void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<InteractionEvidence>

Parameters:

input - a InputStream object.

initialiseXmlParser

protected void initialiseXmlParser(URL url)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<InteractionEvidence>

Parameters:

url - a URL object.

initialiseExpansionMethod

protected void initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)

initialiseExpansionMethod.

Specified by:

initialiseExpansionMethod in class AbstractPsiXmlStream<InteractionEvidence>

Parameters:

expansionMethod - a ComplexExpansionMethod object.

createXmlIterator

protected Iterator<InteractionEvidence> createXmlIterator()

createXmlIterator.

Specified by:

createXmlIterator in class AbstractPsiXmlStream<InteractionEvidence>

Returns:

a Iterator object.