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

Class XmlBinarySource

java.lang.Object

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

psidev.psi.mi.jami.xml.model.extension.datasource.AbstractPsiXmlSource<B>

psidev.psi.mi.jami.xml.model.extension.datasource.AbstractPsiXmlBinarySource<Interaction<? extends Participant>,BinaryInteraction>

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

All Implemented Interfaces:

ErrorHandler, BinaryInteractionSource<BinaryInteraction>, BinaryInteractionStream<BinaryInteraction>, InteractionSource<BinaryInteraction>, InteractionStream<BinaryInteraction>, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlSource<BinaryInteraction>, PsiXmlStreamSource<BinaryInteraction>

public class XmlBinarySource
extends AbstractPsiXmlBinarySource<Interaction<? extends Participant>,BinaryInteraction>
implements BinaryInteractionSource<BinaryInteraction>

PSI-XML data source that provides binary interactions (mixed of abstract interactions and interaction evidences). It will load the full interaction dataset

Since:

08/11/13

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

Method Summary

Modifier and Type	Method	Description
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.AbstractPsiXmlBinarySource

getComplexExpansion, initialiseExpansionMethod

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

close, createXmlIterator, getInteractions, getInteractionsIterator, getNumberOfInteractions, reset

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

error, fatalError, getElementCache, getFileParserListener, 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, 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 org.xml.sax.ErrorHandler

error, fatalError, warning

Methods inherited from interface psidev.psi.mi.jami.datasource.InteractionSource

getInteractions, getNumberOfInteractions

Methods inherited from interface psidev.psi.mi.jami.datasource.InteractionStream

getInteractionsIterator

Methods inherited from interface psidev.psi.mi.jami.datasource.MIDataSource

close, initialiseContext, reset

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

getFileParserListener, setFileParserListener, validateSyntax, validateSyntax

Methods inherited from interface psidev.psi.mi.jami.listener.MIFileParserListener

onAliasWithoutName, onAnnotationWithoutTopic, onInteractionWithoutParticipants, onInvalidOrganismTaxid, onInvalidPosition, onInvalidRange, onInvalidStoichiometry, onInvalidSyntax, onMissingChecksumMethod, onMissingChecksumValue, onMissingConfidenceType, onMissingConfidenceValue, onMissingCvTermName, onMissingInteractorName, onMissingParameterType, onMissingParameterValue, onParticipantWithoutInteractor, onSyntaxWarning, onXrefWithoutDatabase, onXrefWithoutId

Methods inherited from interface psidev.psi.mi.jami.xml.listener.PsiXmlParserListener

onSeveralExperimentalRolesFound, onSeveralExperimentsFound, onSeveralExpressedInOrganismFound, onSeveralHostOrganismFound, onUnresolvedReference

Constructor Detail

XmlBinarySource

public XmlBinarySource()

Constructor for XmlBinarySource.

XmlBinarySource

public XmlBinarySource(File file)

Constructor for XmlBinarySource.

Parameters:

file - a File object.

XmlBinarySource

public XmlBinarySource(InputStream input)

Constructor for XmlBinarySource.

Parameters:

input - a InputStream object.

XmlBinarySource

public XmlBinarySource(Reader reader)

Constructor for XmlBinarySource.

Parameters:

reader - a Reader object.

XmlBinarySource

public XmlBinarySource(URL url)

Constructor for XmlBinarySource.

Parameters:

url - a URL object.

Method Detail

initialiseXmlParser

protected void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteraction>

Parameters:

reader - a Reader object.

initialiseXmlParser

protected void initialiseXmlParser(File file)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteraction>

Parameters:

file - a File object.

initialiseXmlParser

protected void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteraction>

Parameters:

input - a InputStream object.

initialiseXmlParser

protected void initialiseXmlParser(URL url)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteraction>

Parameters:

url - a URL object.