Package psidev.psi.mi.jami.xml.io.writer.compact.extended

Class CompactXmlEvidenceWriter

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.AbstractXmlWriter<T>

psidev.psi.mi.jami.xml.io.writer.compact.AbstractCompactXmlWriter<InteractionEvidence>

psidev.psi.mi.jami.xml.io.writer.compact.extended.CompactXmlEvidenceWriter

All Implemented Interfaces:

InteractionWriter<InteractionEvidence>

public class CompactXmlEvidenceWriter
extends AbstractCompactXmlWriter<InteractionEvidence>

Compact PSI-XML writer for expanded interaction evidences (full experimental evidences)

Since:

19/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
CompactXmlEvidenceWriter(PsiXmlVersion version)	Constructor for CompactXmlEvidenceWriter.
CompactXmlEvidenceWriter(PsiXmlVersion version, File file)	Constructor for CompactXmlEvidenceWriter.
CompactXmlEvidenceWriter(PsiXmlVersion version, OutputStream output)	Constructor for CompactXmlEvidenceWriter.
CompactXmlEvidenceWriter(PsiXmlVersion version, Writer writer)	Constructor for CompactXmlEvidenceWriter.
CompactXmlEvidenceWriter(PsiXmlVersion version, XMLStreamWriter streamWriter, PsiXmlObjectCache cache)	Constructor for CompactXmlEvidenceWriter.

Method Summary

Modifier and Type	Method	Description
protected Source	extractSourceFromInteraction()	extractSourceFromInteraction.
protected void	initialiseDefaultSource()	initialiseDefaultSource.
protected void	initialiseSubWriters()	initialiseSubWriters.
protected void	registerAvailabilities(InteractionEvidence interaction)	registerAvailabilities.
protected void	registerExperiment(InteractionEvidence interaction)	registerExperiment.

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.compact.AbstractCompactXmlWriter

close, getAvailabilities, getAvailabilityWriter, getExperiments, getExperimentWriter, getInteractionType, getInteractors, getInteractorWriter, initialiseContext, initialiseDefaultAvailabilitySet, initialiseDefaultElementCache, initialiseDefaultExperimentSet, initialiseDefaultInteractorSet, initialiseOptionalWriters, registerAllInteractionsProperties, registerAllInteractors, registerAllInteractorsAndExperimentsFrom, registerInteractionProperties, registerParticipantInteractor, registerParticipantPoolInteractor, reset, setAvailabilitySet, setAvailabilityWriter, setExperimentSet, setExperimentWriter, setInteractorSet, setInteractorWriter, writeStartEntryContent

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.AbstractXmlWriter

end, flush, getComplexWriter, getCurrentInteraction, getCurrentSource, getElementCache, getInteractionsIterator, getInteractionWriter, getProcessedInteractions, getStreamWriter, getSubWritersFactory, getVersion, initialiseDefaultInteractionSet, initialiseSubWriters, isStarted, newXmlSource, setAnnotationsWriter, setComplexWriter, setCurrentInteraction, setCurrentSource, setDefaultReleaseDate, setDefaultSource, setElementCache, setEntryAnnotations, setInteractionSet, setInteractionsIterator, setInteractionWriter, setSourceWriter, setStarted, setSubWritersFactory, setVersion, setWriteComplexesAsInteractors, start, write, write, write, writeComplex, writeComplexesAsInteractors, writeEndEntry, writeEndEntryContent, writeEndInteractionList, writeEntryAttributes, writeEntrySetAttributes, writeInteraction, writeInteractionListContent, writeSource, writeStartEntry, writeStartInteractionList, writeSubComplexInEntry

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CompactXmlEvidenceWriter

public CompactXmlEvidenceWriter(PsiXmlVersion version)

Constructor for CompactXmlEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

CompactXmlEvidenceWriter

public CompactXmlEvidenceWriter(PsiXmlVersion version,
                                File file)
                         throws IOException,
                                XMLStreamException

Constructor for CompactXmlEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

CompactXmlEvidenceWriter

public CompactXmlEvidenceWriter(PsiXmlVersion version,
                                OutputStream output)
                         throws XMLStreamException

Constructor for CompactXmlEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

CompactXmlEvidenceWriter

public CompactXmlEvidenceWriter(PsiXmlVersion version,
                                Writer writer)
                         throws XMLStreamException

Constructor for CompactXmlEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a Writer object.

Throws:

XMLStreamException - if any.

CompactXmlEvidenceWriter

public CompactXmlEvidenceWriter(PsiXmlVersion version,
                                XMLStreamWriter streamWriter,
                                PsiXmlObjectCache cache)

Constructor for CompactXmlEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

streamWriter - a XMLStreamWriter object.

cache - a PsiXmlObjectCache object.

Method Detail

registerAvailabilities

protected void registerAvailabilities(InteractionEvidence interaction)

registerAvailabilities.

Specified by:

registerAvailabilities in class AbstractCompactXmlWriter<InteractionEvidence>

Parameters:

interaction - a T object.

registerExperiment

protected void registerExperiment(InteractionEvidence interaction)

registerExperiment.

Specified by:

registerExperiment in class AbstractCompactXmlWriter<InteractionEvidence>

Parameters:

interaction - a T object.

extractSourceFromInteraction

protected Source extractSourceFromInteraction()

extractSourceFromInteraction.

Overrides:

extractSourceFromInteraction in class AbstractXmlWriter<InteractionEvidence>

Returns:

a Source object.

initialiseSubWriters

protected void initialiseSubWriters()

initialiseSubWriters.

Specified by:

initialiseSubWriters in class AbstractXmlWriter<InteractionEvidence>

initialiseDefaultSource

protected void initialiseDefaultSource()

initialiseDefaultSource.

Overrides:

initialiseDefaultSource in class AbstractXmlWriter<InteractionEvidence>