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

Class XmlStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

ErrorHandler, InteractionStream<Interaction>, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlStreamSource<Interaction>

public class XmlStreamSource
extends AbstractPsiXmlStream<Interaction>

Datasource for PSI-xml returning mix of abstract interactions and interaction evidences

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

Method Summary

Modifier and Type	Method	Description
protected Iterator<Interaction>	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

Constructor Detail

XmlStreamSource

public XmlStreamSource()

Constructor for XmlStreamSource.

XmlStreamSource

public XmlStreamSource(File file)

Constructor for XmlStreamSource.

Parameters:

file - a File object.

XmlStreamSource

public XmlStreamSource(InputStream input)

Constructor for XmlStreamSource.

Parameters:

input - a InputStream object.

XmlStreamSource

public XmlStreamSource(Reader reader)

Constructor for XmlStreamSource.

Parameters:

reader - a Reader object.

XmlStreamSource

public XmlStreamSource(URL url)

Constructor for XmlStreamSource.

Parameters:

url - a URL object.

Method Detail

initialiseXmlParser

protected void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Interaction>

Parameters:

reader - a Reader object.

initialiseXmlParser

protected void initialiseXmlParser(File file)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Interaction>

Parameters:

file - a File object.

initialiseXmlParser

protected void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Interaction>

Parameters:

input - a InputStream object.

initialiseXmlParser

protected void initialiseXmlParser(URL url)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Interaction>

Parameters:

url - a URL object.

initialiseExpansionMethod

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

initialiseExpansionMethod.

Specified by:

initialiseExpansionMethod in class AbstractPsiXmlStream<Interaction>

Parameters:

expansionMethod - a ComplexExpansionMethod object.

createXmlIterator

protected Iterator<Interaction> createXmlIterator()

createXmlIterator.

Specified by:

createXmlIterator in class AbstractPsiXmlStream<Interaction>

Returns:

a Iterator object.