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

Class AbstractPsiXmlSource<T extends Interaction>

java.lang.Object

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

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

All Implemented Interfaces:

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

Direct Known Subclasses:

AbstractPsiXmlBinarySource, LightXmlSource, XmlComplexSource, XmlEvidenceSource, XmlModelledSource, XmlSource

public abstract class AbstractPsiXmlSource<T extends Interaction>
extends AbstractPsiXmlStream<T>
implements PsiXmlSource<T>

Abstract class for a PSI-XML datasource that 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

Modifier	Constructor	Description
protected	AbstractPsiXmlSource()	Constructor for AbstractPsiXmlSource.
protected	AbstractPsiXmlSource(File file)	Constructor for AbstractPsiXmlSource.
protected	AbstractPsiXmlSource(InputStream input)	Constructor for AbstractPsiXmlSource.
protected	AbstractPsiXmlSource(Reader reader)	Constructor for AbstractPsiXmlSource.
protected	AbstractPsiXmlSource(URL url)	Constructor for AbstractPsiXmlSource.

Method Summary

Modifier and Type	Method	Description
void	close()	This method close the file data source and all opened streams and readers
protected Iterator<T>	createXmlIterator()	createXmlIterator.
Collection<T>	getInteractions()	The collection of Interactions for this datasource
Iterator<T>	getInteractionsIterator()	The iterator of Interactions for this datasource
long	getNumberOfInteractions()	getNumberOfInteractions
void	reset()	This method will reset the data sources from all loaded options.

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

error, fatalError, getElementCache, getFileParserListener, getInteractorFactory, getParser, initialiseContext, initialiseExpansionMethod, 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.MIDataSource

initialiseContext

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

AbstractPsiXmlSource

protected AbstractPsiXmlSource()

Constructor for AbstractPsiXmlSource.

AbstractPsiXmlSource

protected AbstractPsiXmlSource(File file)

Constructor for AbstractPsiXmlSource.

Parameters:

file - a File object.

AbstractPsiXmlSource

protected AbstractPsiXmlSource(InputStream input)

Constructor for AbstractPsiXmlSource.

Parameters:

input - a InputStream object.

AbstractPsiXmlSource

protected AbstractPsiXmlSource(Reader reader)

Constructor for AbstractPsiXmlSource.

Parameters:

reader - a Reader object.

AbstractPsiXmlSource

protected AbstractPsiXmlSource(URL url)

Constructor for AbstractPsiXmlSource.

Parameters:

url - a URL object.

Method Detail

getInteractions

public Collection<T> getInteractions()
                              throws MIIOException

The collection of Interactions for this datasource

Specified by:

getInteractions in interface InteractionSource<T extends Interaction>

Returns:

collection of Interactions for this datasource

Throws:

MIIOException - if any.

getNumberOfInteractions

public long getNumberOfInteractions()

getNumberOfInteractions

Specified by:

getNumberOfInteractions in interface InteractionSource<T extends Interaction>

Returns:

a long.

getInteractionsIterator

public Iterator<T> getInteractionsIterator()
                                    throws MIIOException

The iterator of Interactions for this datasource

Specified by:

getInteractionsIterator in interface InteractionStream<T extends Interaction>

Overrides:

getInteractionsIterator in class AbstractPsiXmlStream<T extends Interaction>

Returns:

iterator of Interactions for this datasource

Throws:

MIIOException - exception thrown when it cannot iterate MI data

close

public void close()
           throws MIIOException

This method close the file data source and all opened streams and readers

Specified by:

close in interface MIDataSource

Overrides:

close in class AbstractPsiXmlStream<T extends Interaction>

Throws:

MIIOException - if the dataSource cannot be closed

reset

public void reset()
           throws MIIOException

This method will reset the data sources from all loaded options. The data source will be back to what is was before the initialiseContext was called. To re-use the data source after calling the reset() method, the data source needs to be re-initialised with initialiseContext. Any provided inputStream or reader will not be closed and will have to be closed separately.

Specified by:

reset in interface MIDataSource

Overrides:

reset in class AbstractPsiXmlStream<T extends Interaction>

Throws:

MIIOException - if the dataSource cannot be reset

createXmlIterator

protected Iterator<T> createXmlIterator()

createXmlIterator.

Specified by:

createXmlIterator in class AbstractPsiXmlStream<T extends Interaction>

Returns:

a Iterator object.