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

Class AbstractCompactXmlWriter<T extends Interaction>

java.lang.Object

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

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

All Implemented Interfaces:

InteractionWriter<T>

Direct Known Subclasses:

AbstractCompactXmlMixWriter, CompactXmlBinaryEvidenceWriter, CompactXmlBinaryEvidenceWriter, CompactXmlComplexWriter, CompactXmlComplexWriter, CompactXmlEvidenceWriter, CompactXmlEvidenceWriter, CompactXmlModelledBinaryWriter, CompactXmlModelledBinaryWriter, CompactXmlModelledWriter, CompactXmlModelledWriter, CompactXmlNamedBinaryEvidenceWriter, CompactXmlNamedEvidenceWriter, CompactXmlNamedModelledBinaryWriter, CompactXmlNamedModelledWriter, LightCompactXmlBinaryWriter, LightCompactXmlBinaryWriter, LightCompactXmlNamedBinaryWriter, LightCompactXmlNamedWriter, LightCompactXmlWriter, LightCompactXmlWriter

public abstract class AbstractCompactXmlWriter<T extends Interaction>
extends AbstractXmlWriter<T>

Abstract class for Compact XML writers.

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	AbstractCompactXmlWriter(PsiXmlVersion version, Class<T> type)	Constructor for AbstractCompactXmlWriter.
	AbstractCompactXmlWriter(PsiXmlVersion version, Class<T> type, File file)	Constructor for AbstractCompactXmlWriter.
	AbstractCompactXmlWriter(PsiXmlVersion version, Class<T> type, OutputStream output)	Constructor for AbstractCompactXmlWriter.
	AbstractCompactXmlWriter(PsiXmlVersion version, Class<T> type, Writer writer)	Constructor for AbstractCompactXmlWriter.
protected	AbstractCompactXmlWriter(PsiXmlVersion version, Class<T> type, XMLStreamWriter streamWriter, PsiXmlObjectCache elementCache)	Constructor for AbstractCompactXmlWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
protected Set<String>	getAvailabilities()	Getter for the field availabilities.
protected PsiXmlElementWriter<String>	getAvailabilityWriter()	Getter for the field availabilityWriter.
protected Set<Experiment>	getExperiments()	Getter for the field experiments.
protected PsiXmlExperimentWriter	getExperimentWriter()	Getter for the field experimentWriter.
protected Class<T>	getInteractionType()	getInteractionType.
protected Set<Interactor>	getInteractors()	Getter for the field interactors.
protected PsiXmlElementWriter<Interactor>	getInteractorWriter()	Getter for the field interactorWriter.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected void	initialiseDefaultAvailabilitySet()	initialiseDefaultAvailabilitySet.
protected void	initialiseDefaultElementCache()	initialiseDefaultElementCache.
protected void	initialiseDefaultExperimentSet()	initialiseDefaultExperimentSet.
protected void	initialiseDefaultInteractorSet()	initialiseDefaultInteractorSet.
protected void	initialiseOptionalWriters(PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlElementWriter<Interactor> interactorWriter)	initialiseOptionalWriters.
protected void	registerAllInteractionsProperties()	registerAllInteractionsProperties.
protected void	registerAllInteractors(T interaction)	registerAllInteractors.
protected void	registerAllInteractorsAndExperimentsFrom(ModelledInteraction interaction)	registerAllInteractorsAndExperimentsFrom.
protected abstract void	registerAvailabilities(T interaction)	registerAvailabilities.
protected abstract void	registerExperiment(T interaction)	registerExperiment.
protected void	registerInteractionProperties()	registerInteractionProperties.
protected void	registerParticipantInteractor(Entity participant)	registerParticipantInteractor.
protected void	registerParticipantPoolInteractor(ParticipantPool pool)	registerParticipantPoolInteractor.
void	reset()	reset.
void	setAvailabilitySet(Set<String> availabilities)	setAvailabilitySet.
protected void	setAvailabilityWriter(PsiXmlElementWriter<String> availabilityWriter)	Setter for the field availabilityWriter.
void	setExperimentSet(Set<Experiment> experiments)	setExperimentSet.
protected void	setExperimentWriter(PsiXmlExperimentWriter experimentWriter)	Setter for the field experimentWriter.
void	setInteractorSet(Set<Interactor> interactors)	setInteractorSet.
protected void	setInteractorWriter(PsiXmlElementWriter<Interactor> interactorWriter)	Setter for the field interactorWriter.
protected void	writeStartEntryContent()	writeStartEntryContent.

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

end, extractSourceFromInteraction, flush, getComplexWriter, getCurrentInteraction, getCurrentSource, getElementCache, getInteractionsIterator, getInteractionWriter, getProcessedInteractions, getStreamWriter, getSubWritersFactory, getVersion, initialiseDefaultInteractionSet, initialiseDefaultSource, initialiseSubWriters, 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

AbstractCompactXmlWriter

public AbstractCompactXmlWriter(PsiXmlVersion version,
                                Class<T> type)

Constructor for AbstractCompactXmlWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

AbstractCompactXmlWriter

public AbstractCompactXmlWriter(PsiXmlVersion version,
                                Class<T> type,
                                File file)
                         throws IOException,
                                XMLStreamException

Constructor for AbstractCompactXmlWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

AbstractCompactXmlWriter

public AbstractCompactXmlWriter(PsiXmlVersion version,
                                Class<T> type,
                                OutputStream output)
                         throws XMLStreamException

Constructor for AbstractCompactXmlWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

AbstractCompactXmlWriter

public AbstractCompactXmlWriter(PsiXmlVersion version,
                                Class<T> type,
                                Writer writer)
                         throws XMLStreamException

Constructor for AbstractCompactXmlWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

writer - a Writer object.

Throws:

XMLStreamException - if any.

AbstractCompactXmlWriter

protected AbstractCompactXmlWriter(PsiXmlVersion version,
                                   Class<T> type,
                                   XMLStreamWriter streamWriter,
                                   PsiXmlObjectCache elementCache)

Constructor for AbstractCompactXmlWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

streamWriter - a XMLStreamWriter object.

elementCache - a PsiXmlObjectCache object.

Method Detail

initialiseContext

public void initialiseContext(Map<String,Object> options)

Initialise the context of the InteractionWriter given a map of options

Specified by:

initialiseContext in interface InteractionWriter<T extends Interaction>

Overrides:

initialiseContext in class AbstractXmlWriter<T extends Interaction>

Parameters:

options - : the options given by the user

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<T extends Interaction>

Overrides:

close in class AbstractXmlWriter<T extends Interaction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<T extends Interaction>

Overrides:

reset in class AbstractXmlWriter<T extends Interaction>

Throws:

MIIOException - if any.

setExperimentSet

public void setExperimentSet(Set<Experiment> experiments)

setExperimentSet.

Parameters:

experiments - a Set object.

setAvailabilitySet

public void setAvailabilitySet(Set<String> availabilities)

setAvailabilitySet.

Parameters:

availabilities - a Set object.

setInteractorSet

public void setInteractorSet(Set<Interactor> interactors)

setInteractorSet.

Parameters:

interactors - a Set object.

initialiseOptionalWriters

protected void initialiseOptionalWriters(PsiXmlExperimentWriter experimentWriter,
                                         PsiXmlElementWriter<String> availabilityWriter,
                                         PsiXmlElementWriter<Interactor> interactorWriter)

initialiseOptionalWriters.

Specified by:

initialiseOptionalWriters in class AbstractXmlWriter<T extends Interaction>

Parameters:

experimentWriter - a PsiXmlExperimentWriter object.

availabilityWriter - a PsiXmlElementWriter object.

interactorWriter - a PsiXmlElementWriter object.

registerAllInteractionsProperties

protected void registerAllInteractionsProperties()

registerAllInteractionsProperties.

registerAllInteractors

protected void registerAllInteractors(T interaction)

registerAllInteractors.

Parameters:

interaction - a T object.

registerParticipantPoolInteractor

protected void registerParticipantPoolInteractor(ParticipantPool pool)

registerParticipantPoolInteractor.

Parameters:

pool - a ParticipantPool object.

registerParticipantInteractor

protected void registerParticipantInteractor(Entity participant)

registerParticipantInteractor.

Parameters:

participant - a Entity object.

registerAllInteractorsAndExperimentsFrom

protected void registerAllInteractorsAndExperimentsFrom(ModelledInteraction interaction)

registerAllInteractorsAndExperimentsFrom.

Parameters:

interaction - a ModelledInteraction object.

registerAvailabilities

protected abstract void registerAvailabilities(T interaction)

registerAvailabilities.

Parameters:

interaction - a T object.

registerExperiment

protected abstract void registerExperiment(T interaction)

registerExperiment.

Parameters:

interaction - a T object.

writeStartEntryContent

protected void writeStartEntryContent()
                               throws XMLStreamException

writeStartEntryContent.

Specified by:

writeStartEntryContent in class AbstractXmlWriter<T extends Interaction>

Throws:

XMLStreamException - if any.

getAvailabilityWriter

protected PsiXmlElementWriter<String> getAvailabilityWriter()

Getter for the field availabilityWriter.

Returns:

a PsiXmlElementWriter object.

setAvailabilityWriter

protected void setAvailabilityWriter(PsiXmlElementWriter<String> availabilityWriter)

Setter for the field availabilityWriter.

Parameters:

availabilityWriter - a PsiXmlElementWriter object.

getExperimentWriter

protected PsiXmlExperimentWriter getExperimentWriter()

Getter for the field experimentWriter.

Returns:

a PsiXmlExperimentWriter object.

setExperimentWriter

protected void setExperimentWriter(PsiXmlExperimentWriter experimentWriter)

Setter for the field experimentWriter.

Parameters:

experimentWriter - a PsiXmlExperimentWriter object.

getInteractorWriter

protected PsiXmlElementWriter<Interactor> getInteractorWriter()

Getter for the field interactorWriter.

Returns:

a PsiXmlElementWriter object.

setInteractorWriter

protected void setInteractorWriter(PsiXmlElementWriter<Interactor> interactorWriter)

Setter for the field interactorWriter.

Parameters:

interactorWriter - a PsiXmlElementWriter object.

initialiseDefaultExperimentSet

protected void initialiseDefaultExperimentSet()

initialiseDefaultExperimentSet.

initialiseDefaultInteractorSet

protected void initialiseDefaultInteractorSet()

initialiseDefaultInteractorSet.

initialiseDefaultAvailabilitySet

protected void initialiseDefaultAvailabilitySet()

initialiseDefaultAvailabilitySet.

getExperiments

protected Set<Experiment> getExperiments()

Getter for the field experiments.

Returns:

a Set object.

getAvailabilities

protected Set<String> getAvailabilities()

Getter for the field availabilities.

Returns:

a Set object.

getInteractors

protected Set<Interactor> getInteractors()

Getter for the field interactors.

Returns:

a Set object.

initialiseDefaultElementCache

protected void initialiseDefaultElementCache()

initialiseDefaultElementCache.

Specified by:

initialiseDefaultElementCache in class AbstractXmlWriter<T extends Interaction>

getInteractionType

protected Class<T> getInteractionType()

getInteractionType.

Returns:

a Class object.

registerInteractionProperties

protected void registerInteractionProperties()

registerInteractionProperties.