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

Class XmlComplexStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

ErrorHandler, ComplexStream, InteractionStream<Complex>, InteractorStream<Complex>, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlStreamSource<Complex>

public class XmlComplexStreamSource
extends AbstractPsiXmlStream<Complex>
implements ComplexStream

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

Method Summary

Modifier and Type	Method	Description
protected Iterator<Complex>	createXmlIterator()	createXmlIterator.
Iterator<Complex>	getInteractorsIterator()	The interactors iterator for this datasource.
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

XmlComplexStreamSource

public XmlComplexStreamSource()

Constructor for XmlComplexStreamSource.

XmlComplexStreamSource

public XmlComplexStreamSource(File file)

Constructor for XmlComplexStreamSource.

Parameters:

file - a File object.

XmlComplexStreamSource

public XmlComplexStreamSource(InputStream input)

Constructor for XmlComplexStreamSource.

Parameters:

input - a InputStream object.

XmlComplexStreamSource

public XmlComplexStreamSource(Reader reader)

Constructor for XmlComplexStreamSource.

Parameters:

reader - a Reader object.

XmlComplexStreamSource

public XmlComplexStreamSource(URL url)

Constructor for XmlComplexStreamSource.

Parameters:

url - a URL object.

Method Detail

initialiseXmlParser

protected void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Complex>

Parameters:

reader - a Reader object.

initialiseXmlParser

protected void initialiseXmlParser(File file)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Complex>

Parameters:

file - a File object.

initialiseXmlParser

protected void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Complex>

Parameters:

input - a InputStream object.

initialiseXmlParser

protected void initialiseXmlParser(URL url)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<Complex>

Parameters:

url - a URL object.

initialiseExpansionMethod

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

initialiseExpansionMethod.

Specified by:

initialiseExpansionMethod in class AbstractPsiXmlStream<Complex>

Parameters:

expansionMethod - a ComplexExpansionMethod object.

createXmlIterator

protected Iterator<Complex> createXmlIterator()

createXmlIterator.

Specified by:

createXmlIterator in class AbstractPsiXmlStream<Complex>

Returns:

a Iterator object.

getInteractorsIterator

public Iterator<Complex> getInteractorsIterator()
                                         throws MIIOException

The interactors iterator for this datasource.

Specified by:

getInteractorsIterator in interface InteractorStream<Complex>

Returns:

iterator of interactors for a given datasource

Throws:

MIIOException - if any.