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

Class CompactXmlComplexWriter

java.lang.Object

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

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

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

All Implemented Interfaces:

InteractionWriter<Complex>

public class CompactXmlComplexWriter
extends AbstractCompactXmlWriter<Complex>

Compact PSI-XML writer for named biological complexes (no experimental evidences). Participants, features, experiments also have expanded names

Since:

19/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

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

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, 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

CompactXmlComplexWriter

public CompactXmlComplexWriter(PsiXmlVersion version)

Constructor for CompactXmlComplexWriter.

Parameters:

version - a PsiXmlVersion object.

CompactXmlComplexWriter

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

Constructor for CompactXmlComplexWriter.

Parameters:

version - a PsiXmlVersion object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

CompactXmlComplexWriter

public CompactXmlComplexWriter(PsiXmlVersion version,
                               OutputStream output)
                        throws XMLStreamException

Constructor for CompactXmlComplexWriter.

Parameters:

version - a PsiXmlVersion object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

CompactXmlComplexWriter

public CompactXmlComplexWriter(PsiXmlVersion version,
                               Writer writer)
                        throws XMLStreamException

Constructor for CompactXmlComplexWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a Writer object.

Throws:

XMLStreamException - if any.

CompactXmlComplexWriter

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

Constructor for CompactXmlComplexWriter.

Parameters:

version - a PsiXmlVersion object.

streamWriter - a XMLStreamWriter object.

cache - a PsiXmlObjectCache object.

Method Detail

registerAvailabilities

protected void registerAvailabilities(Complex interaction)

registerAvailabilities.

Specified by:

registerAvailabilities in class AbstractCompactXmlWriter<Complex>

Parameters:

interaction - a T object.

registerExperiment

protected void registerExperiment(Complex interaction)

registerExperiment.

Specified by:

registerExperiment in class AbstractCompactXmlWriter<Complex>

Parameters:

interaction - a T object.

registerInteractionProperties

protected void registerInteractionProperties()

registerInteractionProperties.

Overrides:

registerInteractionProperties in class AbstractCompactXmlWriter<Complex>

extractSourceFromInteraction

protected Source extractSourceFromInteraction()

extractSourceFromInteraction.

Overrides:

extractSourceFromInteraction in class AbstractXmlWriter<Complex>

Returns:

a Source object.

initialiseSubWriters

protected void initialiseSubWriters()

initialiseSubWriters.

Specified by:

initialiseSubWriters in class AbstractXmlWriter<Complex>