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

Class XmlComplexSource

java.lang.Object

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

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

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

All Implemented Interfaces:

ErrorHandler, ComplexSource, InteractionSource<Complex>, InteractionStream<Complex>, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlSource<Complex>, PsiXmlStreamSource<Complex>

public class XmlComplexSource
extends AbstractPsiXmlSource<Complex>
implements ComplexSource

PSI-XML data source that provides abstract interactions (ignore full 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
XmlComplexSource()	Constructor for XmlComplexSource.
XmlComplexSource(File file)	Constructor for XmlComplexSource.
XmlComplexSource(InputStream input)	Constructor for XmlComplexSource.
XmlComplexSource(Reader reader)	Constructor for XmlComplexSource.
XmlComplexSource(URL url)	Constructor for XmlComplexSource.

Method Summary

Modifier and Type	Method	Description
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.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

XmlComplexSource

public XmlComplexSource()

Constructor for XmlComplexSource.

XmlComplexSource

public XmlComplexSource(File file)

Constructor for XmlComplexSource.

Parameters:

file - a File object.

XmlComplexSource

public XmlComplexSource(InputStream input)

Constructor for XmlComplexSource.

Parameters:

input - a InputStream object.

XmlComplexSource

public XmlComplexSource(Reader reader)

Constructor for XmlComplexSource.

Parameters:

reader - a Reader object.

XmlComplexSource

public XmlComplexSource(URL url)

Constructor for XmlComplexSource.

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.