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

Class AbstractCompactXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence>

java.lang.Object

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

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

psidev.psi.mi.jami.xml.io.writer.compact.AbstractCompactXmlMixWriter<I,M,E>

All Implemented Interfaces:

InteractionWriter<I>

Direct Known Subclasses:

CompactXmlBinaryWriter, CompactXmlBinaryWriter, CompactXmlNamedBinaryWriter, CompactXmlNamedWriter, CompactXmlWriter, CompactXmlWriter

public abstract class AbstractCompactXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence>
extends AbstractCompactXmlWriter<I>

Abstract class for a compact PSI-XML writer of mixed interactions

Since:

20/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractCompactXmlMixWriter(PsiXmlVersion version, Class<I> type)	Constructor for AbstractCompactXmlMixWriter.
AbstractCompactXmlMixWriter(PsiXmlVersion version, Class<I> type, File file)	Constructor for AbstractCompactXmlMixWriter.
AbstractCompactXmlMixWriter(PsiXmlVersion version, Class<I> type, OutputStream output)	Constructor for AbstractCompactXmlMixWriter.
AbstractCompactXmlMixWriter(PsiXmlVersion version, Class<I> type, Writer writer)	Constructor for AbstractCompactXmlMixWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	flush()	Flushes the writer (commit or write on disk)
protected abstract void	initialiseDelegateWriters()	initialiseDelegateWriters.
protected void	initialiseSubWriters()	initialiseSubWriters.
protected void	registerAvailabilities(I interaction)	registerAvailabilities.
protected void	registerExperiment(I interaction)	registerExperiment.
void	reset()	reset.
void	setAvailabilitySet(Set<String> availabilities)	setAvailabilitySet.
protected void	setAvailabilityWriter(PsiXmlElementWriter<String> availabilityWriter)	Setter for the field availabilityWriter.
void	setComplexWriter(PsiXmlInteractionWriter<ModelledInteraction> complexWriter)	Setter for the field complexWriter.
void	setDefaultReleaseDate(XMLGregorianCalendar defaultReleaseDate)	Setter for the field defaultReleaseDate.
void	setDefaultSource(Source defaultSource)	Setter for the field defaultSource.
void	setElementCache(PsiXmlObjectCache elementCache)	Setter for the field elementCache.
protected void	setEvidenceWriter(AbstractCompactXmlWriter<E> evidenceWriter)	Setter for the field evidenceWriter.
void	setExperimentSet(Set<Experiment> experiments)	setExperimentSet.
protected void	setExperimentWriter(PsiXmlExperimentWriter experimentWriter)	Setter for the field experimentWriter.
void	setInteractionSet(Set<Interaction> processedInteractions)	setInteractionSet.
void	setInteractorSet(Set<Interactor> interactors)	setInteractorSet.
protected void	setInteractorWriter(PsiXmlElementWriter<Interactor> interactorWriter)	Setter for the field interactorWriter.
protected void	setLightWriter(AbstractCompactXmlWriter<I> lightWriter)	Setter for the field lightWriter.
protected void	setModelledWriter(AbstractCompactXmlWriter<M> modelledWriter)	Setter for the field modelledWriter.
void	setSourceWriter(PsiXmlSourceWriter sourceWriter)	Setter for the field sourceWriter.
void	setVersion(PsiXmlVersion version)	Setter for the field version.
void	setWriteComplexesAsInteractors(boolean writeComplexesAsInteractors)	Setter for the field writeComplexesAsInteractors.
void	write(I interaction)	Writes an interaction
void	write(Collection<? extends I> interactions)	Writes a collection of Interaction objects
void	write(Iterator<? extends I> interactions)	Writes Interaction objects using iterator

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

getAvailabilities, getAvailabilityWriter, getExperiments, getExperimentWriter, getInteractionType, getInteractors, getInteractorWriter, initialiseContext, initialiseDefaultAvailabilitySet, initialiseDefaultElementCache, initialiseDefaultExperimentSet, initialiseDefaultInteractorSet, initialiseOptionalWriters, registerAllInteractionsProperties, registerAllInteractors, registerAllInteractorsAndExperimentsFrom, registerInteractionProperties, registerParticipantInteractor, registerParticipantPoolInteractor, writeStartEntryContent

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

end, extractSourceFromInteraction, getComplexWriter, getCurrentInteraction, getCurrentSource, getElementCache, getInteractionsIterator, getInteractionWriter, getProcessedInteractions, getStreamWriter, getSubWritersFactory, getVersion, initialiseDefaultInteractionSet, initialiseDefaultSource, initialiseSubWriters, isStarted, newXmlSource, setAnnotationsWriter, setCurrentInteraction, setCurrentSource, setEntryAnnotations, setInteractionsIterator, setInteractionWriter, setStarted, setSubWritersFactory, start, 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

AbstractCompactXmlMixWriter

public AbstractCompactXmlMixWriter(PsiXmlVersion version,
                                   Class<I> type)

Constructor for AbstractCompactXmlMixWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

AbstractCompactXmlMixWriter

public AbstractCompactXmlMixWriter(PsiXmlVersion version,
                                   Class<I> type,
                                   File file)
                            throws IOException,
                                   XMLStreamException

Constructor for AbstractCompactXmlMixWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

AbstractCompactXmlMixWriter

public AbstractCompactXmlMixWriter(PsiXmlVersion version,
                                   Class<I> type,
                                   OutputStream output)
                            throws XMLStreamException

Constructor for AbstractCompactXmlMixWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

AbstractCompactXmlMixWriter

public AbstractCompactXmlMixWriter(PsiXmlVersion version,
                                   Class<I> type,
                                   Writer writer)
                            throws XMLStreamException

Constructor for AbstractCompactXmlMixWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

writer - a Writer object.

Throws:

XMLStreamException - if any.

Method Detail

initialiseSubWriters

protected void initialiseSubWriters()

initialiseSubWriters.

Specified by:

initialiseSubWriters in class AbstractXmlWriter<I extends Interaction>

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<I extends Interaction>

Overrides:

close in class AbstractCompactXmlWriter<I extends Interaction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<I extends Interaction>

Overrides:

reset in class AbstractCompactXmlWriter<I extends Interaction>

Throws:

MIIOException - if any.

setAvailabilityWriter

protected void setAvailabilityWriter(PsiXmlElementWriter<String> availabilityWriter)

Setter for the field availabilityWriter.

Overrides:

setAvailabilityWriter in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

availabilityWriter - a PsiXmlElementWriter object.

setExperimentWriter

protected void setExperimentWriter(PsiXmlExperimentWriter experimentWriter)

Setter for the field experimentWriter.

Overrides:

setExperimentWriter in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

experimentWriter - a PsiXmlExperimentWriter object.

setInteractorWriter

protected void setInteractorWriter(PsiXmlElementWriter<Interactor> interactorWriter)

Setter for the field interactorWriter.

Overrides:

setInteractorWriter in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

interactorWriter - a PsiXmlElementWriter object.

setExperimentSet

public void setExperimentSet(Set<Experiment> experiments)

setExperimentSet.

Overrides:

setExperimentSet in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

experiments - a Set object.

setAvailabilitySet

public void setAvailabilitySet(Set<String> availabilities)

setAvailabilitySet.

Overrides:

setAvailabilitySet in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

availabilities - a Set object.

setVersion

public void setVersion(PsiXmlVersion version)

Setter for the field version.

Overrides:

setVersion in class AbstractXmlWriter<I extends Interaction>

Parameters:

version - a PsiXmlVersion object.

setInteractorSet

public void setInteractorSet(Set<Interactor> interactors)

setInteractorSet.

Overrides:

setInteractorSet in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

interactors - a Set object.

setInteractionSet

public void setInteractionSet(Set<Interaction> processedInteractions)

setInteractionSet.

Overrides:

setInteractionSet in class AbstractXmlWriter<I extends Interaction>

Parameters:

processedInteractions - a Set object.

setDefaultSource

public void setDefaultSource(Source defaultSource)

Setter for the field defaultSource.

Overrides:

setDefaultSource in class AbstractXmlWriter<I extends Interaction>

Parameters:

defaultSource - a Source object.

setDefaultReleaseDate

public void setDefaultReleaseDate(XMLGregorianCalendar defaultReleaseDate)

Setter for the field defaultReleaseDate.

Overrides:

setDefaultReleaseDate in class AbstractXmlWriter<I extends Interaction>

Parameters:

defaultReleaseDate - a XMLGregorianCalendar object.

flush

public void flush()
           throws MIIOException

Flushes the writer (commit or write on disk)

Specified by:

flush in interface InteractionWriter<I extends Interaction>

Overrides:

flush in class AbstractXmlWriter<I extends Interaction>

Throws:

MIIOException - : if cannot flush

setWriteComplexesAsInteractors

public void setWriteComplexesAsInteractors(boolean writeComplexesAsInteractors)

Setter for the field writeComplexesAsInteractors.

Overrides:

setWriteComplexesAsInteractors in class AbstractXmlWriter<I extends Interaction>

Parameters:

writeComplexesAsInteractors - a boolean.

registerExperiment

protected void registerExperiment(I interaction)

registerExperiment.

Specified by:

registerExperiment in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

interaction - a T object.

registerAvailabilities

protected void registerAvailabilities(I interaction)

registerAvailabilities.

Specified by:

registerAvailabilities in class AbstractCompactXmlWriter<I extends Interaction>

Parameters:

interaction - a T object.

write

public void write(Iterator<? extends I> interactions)
           throws MIIOException

Writes Interaction objects using iterator

Specified by:

write in interface InteractionWriter<I extends Interaction>

Overrides:

write in class AbstractXmlWriter<I extends Interaction>

Parameters:

interactions - : the iterator of interactions to write

Throws:

MIIOException - : if cannot write

write

public void write(Collection<? extends I> interactions)
           throws MIIOException

Writes a collection of Interaction objects

Specified by:

write in interface InteractionWriter<I extends Interaction>

Overrides:

write in class AbstractXmlWriter<I extends Interaction>

Parameters:

interactions - : the interactions to write

Throws:

MIIOException - : if cannot write

write

public void write(I interaction)
           throws MIIOException

Writes an interaction

Specified by:

write in interface InteractionWriter<I extends Interaction>

Overrides:

write in class AbstractXmlWriter<I extends Interaction>

Parameters:

interaction - : the interaction to write

Throws:

MIIOException - : if cannot write

setSourceWriter

public void setSourceWriter(PsiXmlSourceWriter sourceWriter)

Setter for the field sourceWriter.

Overrides:

setSourceWriter in class AbstractXmlWriter<I extends Interaction>

Parameters:

sourceWriter - a PsiXmlSourceWriter object.

setComplexWriter

public void setComplexWriter(PsiXmlInteractionWriter<ModelledInteraction> complexWriter)

Setter for the field complexWriter.

Overrides:

setComplexWriter in class AbstractXmlWriter<I extends Interaction>

Parameters:

complexWriter - a PsiXmlInteractionWriter object.

setElementCache

public void setElementCache(PsiXmlObjectCache elementCache)

Setter for the field elementCache.

Overrides:

setElementCache in class AbstractXmlWriter<I extends Interaction>

Parameters:

elementCache - a PsiXmlObjectCache object.

setEvidenceWriter

protected void setEvidenceWriter(AbstractCompactXmlWriter<E> evidenceWriter)

Setter for the field evidenceWriter.

Parameters:

evidenceWriter - a AbstractCompactXmlWriter object.

setModelledWriter

protected void setModelledWriter(AbstractCompactXmlWriter<M> modelledWriter)

Setter for the field modelledWriter.

Parameters:

modelledWriter - a AbstractCompactXmlWriter object.

setLightWriter

protected void setLightWriter(AbstractCompactXmlWriter<I> lightWriter)

Setter for the field lightWriter.

Parameters:

lightWriter - a AbstractCompactXmlWriter object.

initialiseDelegateWriters

protected abstract void initialiseDelegateWriters()

initialiseDelegateWriters.