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

Class XmlBinaryEvidenceSource

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<InteractionEvidence,BinaryInteractionEvidence>

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

All Implemented Interfaces:

ErrorHandler, BinaryInteractionEvidenceSource, BinaryInteractionEvidenceStream, BinaryInteractionSource<BinaryInteractionEvidence>, BinaryInteractionStream<BinaryInteractionEvidence>, InteractionEvidenceSource<BinaryInteractionEvidence>, InteractionEvidenceStream<BinaryInteractionEvidence>, InteractionSource<BinaryInteractionEvidence>, InteractionStream<BinaryInteractionEvidence>, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlSource<BinaryInteractionEvidence>, PsiXmlStreamSource<BinaryInteractionEvidence>

public class XmlBinaryEvidenceSource
extends AbstractPsiXmlBinarySource<InteractionEvidence,BinaryInteractionEvidence>
implements BinaryInteractionEvidenceSource

PSI-XML data source that provides binary interactions evidence (full experimental details). 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
XmlBinaryEvidenceSource()	Constructor for XmlBinaryEvidenceSource.
XmlBinaryEvidenceSource(File file)	Constructor for XmlBinaryEvidenceSource.
XmlBinaryEvidenceSource(InputStream input)	Constructor for XmlBinaryEvidenceSource.
XmlBinaryEvidenceSource(Reader reader)	Constructor for XmlBinaryEvidenceSource.
XmlBinaryEvidenceSource(URL url)	Constructor for XmlBinaryEvidenceSource.

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

XmlBinaryEvidenceSource

public XmlBinaryEvidenceSource()

Constructor for XmlBinaryEvidenceSource.

XmlBinaryEvidenceSource

public XmlBinaryEvidenceSource(File file)

Constructor for XmlBinaryEvidenceSource.

Parameters:

file - a File object.

XmlBinaryEvidenceSource

public XmlBinaryEvidenceSource(InputStream input)

Constructor for XmlBinaryEvidenceSource.

Parameters:

input - a InputStream object.

XmlBinaryEvidenceSource

public XmlBinaryEvidenceSource(Reader reader)

Constructor for XmlBinaryEvidenceSource.

Parameters:

reader - a Reader object.

XmlBinaryEvidenceSource

public XmlBinaryEvidenceSource(URL url)

Constructor for XmlBinaryEvidenceSource.

Parameters:

url - a URL object.

Method Detail

initialiseXmlParser

protected void initialiseXmlParser(Reader reader)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteractionEvidence>

Parameters:

reader - a Reader object.

initialiseXmlParser

protected void initialiseXmlParser(File file)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteractionEvidence>

Parameters:

file - a File object.

initialiseXmlParser

protected void initialiseXmlParser(InputStream input)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteractionEvidence>

Parameters:

input - a InputStream object.

initialiseXmlParser

protected void initialiseXmlParser(URL url)

initialiseXmlParser.

Specified by:

initialiseXmlParser in class AbstractPsiXmlStream<BinaryInteractionEvidence>

Parameters:

url - a URL object.