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

Class CompactXmlNamedEvidenceWriter

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.CompactXmlNamedEvidenceWriter

All Implemented Interfaces:

InteractionWriter<InteractionEvidence>

public class CompactXmlNamedEvidenceWriter
extends AbstractCompactXmlWriter<InteractionEvidence>

Compact PSI-XML writer for named interaction evidences (full experimental evidences) Participants, features and experiments also have expanded names to write

Since:

19/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected Source	extractSourceFromInteraction()	extractSourceFromInteraction.
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, initialiseDefaultSource, 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

CompactXmlNamedEvidenceWriter

public CompactXmlNamedEvidenceWriter(PsiXmlVersion version)

Constructor for CompactXmlNamedEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

CompactXmlNamedEvidenceWriter

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

Constructor for CompactXmlNamedEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

CompactXmlNamedEvidenceWriter

public CompactXmlNamedEvidenceWriter(PsiXmlVersion version,
                                     OutputStream output)
                              throws XMLStreamException

Constructor for CompactXmlNamedEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

CompactXmlNamedEvidenceWriter

public CompactXmlNamedEvidenceWriter(PsiXmlVersion version,
                                     Writer writer)
                              throws XMLStreamException

Constructor for CompactXmlNamedEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a Writer object.

Throws:

XMLStreamException - if any.

CompactXmlNamedEvidenceWriter

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

Constructor for CompactXmlNamedEvidenceWriter.

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>