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

Class XmlModelledStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

ErrorHandler, InteractionStream<ModelledInteraction>, MIDataSource, MIFileDataSource, ModelledInteractionStream<ModelledInteraction>, MIFileParserListener, PsiXmlParserListener, PsiXmlStreamSource<ModelledInteraction>

public class XmlModelledStreamSource
extends AbstractPsiXmlStream<ModelledInteraction>
implements ModelledInteractionStream<ModelledInteraction>

Datasource for Psi-XML abstract interactions

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

Method Summary

Modifier and Type	Method	Description
protected Iterator<ModelledInteraction>	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

XmlModelledStreamSource

public XmlModelledStreamSource()

Constructor for XmlModelledStreamSource.

XmlModelledStreamSource

public XmlModelledStreamSource(File file)

Constructor for XmlModelledStreamSource.

Parameters:

file - a File object.

XmlModelledStreamSource

public XmlModelledStreamSource(InputStream input)

Constructor for XmlModelledStreamSource.

Parameters:

input - a InputStream object.

XmlModelledStreamSource

public XmlModelledStreamSource(Reader reader)

Constructor for XmlModelledStreamSource.

Parameters:

reader - a Reader object.

XmlModelledStreamSource

public XmlModelledStreamSource(URL url)

Constructor for XmlModelledStreamSource.

Parameters:

url - a URL object.

Method Detail

initialiseXmlParser

protected void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledInteraction>

Parameters:

reader - a Reader object.

initialiseXmlParser

protected void initialiseXmlParser(File file)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledInteraction>

Parameters:

file - a File object.

initialiseXmlParser

protected void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledInteraction>

Parameters:

input - a InputStream object.

initialiseXmlParser

protected void initialiseXmlParser(URL url)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledInteraction>

Parameters:

url - a URL object.

initialiseExpansionMethod

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

initialiseExpansionMethod.

Specified by:

initialiseExpansionMethod in class AbstractPsiXmlStream<ModelledInteraction>

Parameters:

expansionMethod - a ComplexExpansionMethod object.

createXmlIterator

protected Iterator<ModelledInteraction> createXmlIterator()

createXmlIterator.

Specified by:

createXmlIterator in class AbstractPsiXmlStream<ModelledInteraction>

Returns:

a Iterator object.