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

Class XmlModelledBinarySource

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<ModelledInteraction,ModelledBinaryInteraction>

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

All Implemented Interfaces:

ErrorHandler, BinaryInteractionSource<ModelledBinaryInteraction>, BinaryInteractionStream<ModelledBinaryInteraction>, InteractionSource<ModelledBinaryInteraction>, InteractionStream<ModelledBinaryInteraction>, MIDataSource, MIFileDataSource, ModelledBinaryInteractionSource, ModelledInteractionSource<ModelledBinaryInteraction>, ModelledInteractionStream<ModelledBinaryInteraction>, MIFileParserListener, PsiXmlParserListener, PsiXmlSource<ModelledBinaryInteraction>, PsiXmlStreamSource<ModelledBinaryInteraction>

public class XmlModelledBinarySource
extends AbstractPsiXmlBinarySource<ModelledInteraction,ModelledBinaryInteraction>
implements ModelledBinaryInteractionSource

PSI-XML data source that provides modelled binary interactions (ignore experimental details). It will load the full interaction dataset

Since:

11/11/13

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

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

XmlModelledBinarySource

public XmlModelledBinarySource()

Constructor for XmlModelledBinarySource.

XmlModelledBinarySource

public XmlModelledBinarySource(File file)

Constructor for XmlModelledBinarySource.

Parameters:

file - a File object.

XmlModelledBinarySource

public XmlModelledBinarySource(InputStream input)

Constructor for XmlModelledBinarySource.

Parameters:

input - a InputStream object.

XmlModelledBinarySource

public XmlModelledBinarySource(Reader reader)

Constructor for XmlModelledBinarySource.

Parameters:

reader - a Reader object.

XmlModelledBinarySource

public XmlModelledBinarySource(URL url)

Constructor for XmlModelledBinarySource.

Parameters:

url - a URL object.

Method Detail

initialiseXmlParser

protected void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledBinaryInteraction>

Parameters:

reader - a Reader object.

initialiseXmlParser

protected void initialiseXmlParser(File file)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledBinaryInteraction>

Parameters:

file - a File object.

initialiseXmlParser

protected void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledBinaryInteraction>

Parameters:

input - a InputStream object.

initialiseXmlParser

protected void initialiseXmlParser(URL url)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<ModelledBinaryInteraction>

Parameters:

url - a URL object.