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

Class DefaultPsiXmlSource

java.lang.Object

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

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

All Implemented Interfaces:

ErrorHandler, InteractionSource, InteractionStream, MIDataSource, MIFileDataSource, MIFileParserListener, PsiXmlParserListener, PsiXmlSource, PsiXmlStreamSource

public class DefaultPsiXmlSource
extends DefaultPsiXmlStreamSource
implements PsiXmlSource

Generic class for PSI-XML full datasource. This datasource loads all the interactions from a PSI-XML file

Since:

08/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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

FILE_URI_PREFIX, URL_PREFIX_REGEXP

Constructor Summary

Constructors

Constructor	Description
DefaultPsiXmlSource()	Constructor for DefaultPsiXmlSource.

Method Summary

Modifier and Type	Method	Description
protected PsiXmlSource	getDelegate()	Getter for the field delegate.
Collection<Interaction>	getInteractions()	getInteractions.
long	getNumberOfInteractions()	getNumberOfInteractions.
protected void	initialiseDelegate(Map<String,Object> options, PsiXmlDataSourceFactory factory, InteractionCategory category, ComplexType type)	initialiseDelegate.

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

close, error, fatalError, getFileParserListener, getInteractionsIterator, initialiseContext, 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, reset, setDelegate, setFileParserListener, 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.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

DefaultPsiXmlSource

public DefaultPsiXmlSource()

Constructor for DefaultPsiXmlSource.

Method Detail

initialiseDelegate

protected void initialiseDelegate(Map<String,Object> options,
                                  PsiXmlDataSourceFactory factory,
                                  InteractionCategory category,
                                  ComplexType type)

initialiseDelegate.

Overrides:

initialiseDelegate in class DefaultPsiXmlStreamSource

Parameters:

options - a Map object.

factory - a PsiXmlDataSourceFactory object.

category - a InteractionCategory object.

type - a ComplexType object.

getInteractions

public Collection<Interaction> getInteractions()
                                        throws MIIOException

getInteractions.

Specified by:

getInteractions in interface InteractionSource

Returns:

a Collection object.

Throws:

MIIOException - if any.

getNumberOfInteractions

public long getNumberOfInteractions()

getNumberOfInteractions.

Specified by:

getNumberOfInteractions in interface InteractionSource

Returns:

a long.

getDelegate

protected PsiXmlSource getDelegate()

Getter for the field delegate.

Overrides:

getDelegate in class DefaultPsiXmlStreamSource

Returns:

a PsiXmlStreamSource object.