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

Class CompactXmlNamedBinaryEvidenceWriter

java.lang.Object

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

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

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

All Implemented Interfaces:

InteractionWriter<BinaryInteractionEvidence>

public class CompactXmlNamedBinaryEvidenceWriter
extends AbstractCompactXmlWriter<BinaryInteractionEvidence>

Compact PSI-XML writer for named binary 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
CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version)	Constructor for CompactXmlNamedBinaryEvidenceWriter.
CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version, File file)	Constructor for CompactXmlNamedBinaryEvidenceWriter.
CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version, OutputStream output)	Constructor for CompactXmlNamedBinaryEvidenceWriter.
CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version, Writer writer)	Constructor for CompactXmlNamedBinaryEvidenceWriter.
CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version, XMLStreamWriter streamWriter, PsiXmlObjectCache cache)	Constructor for CompactXmlNamedBinaryEvidenceWriter.

Method Summary

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

CompactXmlNamedBinaryEvidenceWriter

public CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version)

Constructor for CompactXmlNamedBinaryEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

CompactXmlNamedBinaryEvidenceWriter

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

Constructor for CompactXmlNamedBinaryEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

CompactXmlNamedBinaryEvidenceWriter

public CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version,
                                           OutputStream output)
                                    throws XMLStreamException

Constructor for CompactXmlNamedBinaryEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

CompactXmlNamedBinaryEvidenceWriter

public CompactXmlNamedBinaryEvidenceWriter(PsiXmlVersion version,
                                           Writer writer)
                                    throws XMLStreamException

Constructor for CompactXmlNamedBinaryEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a Writer object.

Throws:

XMLStreamException - if any.

CompactXmlNamedBinaryEvidenceWriter

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

Constructor for CompactXmlNamedBinaryEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

streamWriter - a XMLStreamWriter object.

cache - a PsiXmlObjectCache object.

Method Detail

registerAvailabilities

protected void registerAvailabilities(BinaryInteractionEvidence interaction)

registerAvailabilities.

Specified by:

registerAvailabilities in class AbstractCompactXmlWriter<BinaryInteractionEvidence>

Parameters:

interaction - a T object.

registerExperiment

protected void registerExperiment(BinaryInteractionEvidence interaction)

registerExperiment.

Specified by:

registerExperiment in class AbstractCompactXmlWriter<BinaryInteractionEvidence>

Parameters:

interaction - a T object.

extractSourceFromInteraction

protected Source extractSourceFromInteraction()

extractSourceFromInteraction.

Overrides:

extractSourceFromInteraction in class AbstractXmlWriter<BinaryInteractionEvidence>

Returns:

a Source object.

initialiseSubWriters

protected void initialiseSubWriters()

initialiseSubWriters.

Specified by:

initialiseSubWriters in class AbstractXmlWriter<BinaryInteractionEvidence>