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

Class AbstractPsiXmlBinarySource<T extends Interaction,B extends BinaryInteraction>

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<T,B>

All Implemented Interfaces:

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

Direct Known Subclasses:

LightXmlBinarySource, XmlBinaryEvidenceSource, XmlBinarySource, XmlModelledBinarySource

public abstract class AbstractPsiXmlBinarySource<T extends Interaction,B extends BinaryInteraction>
extends AbstractPsiXmlSource<B>
implements BinaryInteractionSource<B>

Abstract class for Psi-XML binary interaction data source which loads 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
AbstractPsiXmlBinarySource()	Constructor for AbstractPsiXmlBinarySource.
AbstractPsiXmlBinarySource(File file)	Constructor for AbstractPsiXmlBinarySource.
AbstractPsiXmlBinarySource(InputStream input)	Constructor for AbstractPsiXmlBinarySource.
AbstractPsiXmlBinarySource(Reader reader)	Constructor for AbstractPsiXmlBinarySource.
AbstractPsiXmlBinarySource(URL url)	Constructor for AbstractPsiXmlBinarySource.

Method Summary

Modifier and Type	Method	Description
protected ComplexExpansionMethod<T,B>	getComplexExpansion()	Getter for the field complexExpansion.
protected void	initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)	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, initialiseXmlParser, initialiseXmlParser, initialiseXmlParser, initialiseXmlParser, 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

AbstractPsiXmlBinarySource

public AbstractPsiXmlBinarySource()

Constructor for AbstractPsiXmlBinarySource.

AbstractPsiXmlBinarySource

public AbstractPsiXmlBinarySource(File file)

Constructor for AbstractPsiXmlBinarySource.

Parameters:

file - a File object.

AbstractPsiXmlBinarySource

public AbstractPsiXmlBinarySource(InputStream input)

Constructor for AbstractPsiXmlBinarySource.

Parameters:

input - a InputStream object.

AbstractPsiXmlBinarySource

public AbstractPsiXmlBinarySource(Reader reader)

Constructor for AbstractPsiXmlBinarySource.

Parameters:

reader - a Reader object.

AbstractPsiXmlBinarySource

public AbstractPsiXmlBinarySource(URL url)

Constructor for AbstractPsiXmlBinarySource.

Parameters:

url - a URL object.

Method Detail

initialiseExpansionMethod

protected void initialiseExpansionMethod(ComplexExpansionMethod<? extends Interaction,? extends BinaryInteraction> expansionMethod)

initialiseExpansionMethod.

Specified by:

initialiseExpansionMethod in class AbstractPsiXmlStream<B extends BinaryInteraction>

Parameters:

expansionMethod - a ComplexExpansionMethod object.

getComplexExpansion

protected ComplexExpansionMethod<T,B> getComplexExpansion()

Getter for the field complexExpansion.

Returns:

a ComplexExpansionMethod object.