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

Class LightXmlStreamSource

java.lang.Object

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

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

All Implemented Interfaces:

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

public class LightXmlStreamSource
extends AbstractPsiXmlStream<Interaction>

Datasource for PSI-xml returning basic 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
LightXmlStreamSource()	Constructor for LightXmlStreamSource.
LightXmlStreamSource(File file)	Constructor for LightXmlStreamSource.
LightXmlStreamSource(InputStream input)	Constructor for LightXmlStreamSource.
LightXmlStreamSource(Reader reader)	Constructor for LightXmlStreamSource.
LightXmlStreamSource(URL url)	Constructor for LightXmlStreamSource.

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

LightXmlStreamSource

public LightXmlStreamSource()

Constructor for LightXmlStreamSource.

LightXmlStreamSource

public LightXmlStreamSource(File file)

Constructor for LightXmlStreamSource.

Parameters:

file - a File object.

LightXmlStreamSource

public LightXmlStreamSource(InputStream input)

Constructor for LightXmlStreamSource.

Parameters:

input - a InputStream object.

LightXmlStreamSource

public LightXmlStreamSource(Reader reader)

Constructor for LightXmlStreamSource.

Parameters:

reader - a Reader object.

LightXmlStreamSource

public LightXmlStreamSource(URL url)

Constructor for LightXmlStreamSource.

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.