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

Class AbstractXmlWriter<T extends Interaction>

java.lang.Object

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

All Implemented Interfaces:

InteractionWriter<T>

Direct Known Subclasses:

AbstractCompactXmlWriter, AbstractExpandedXmlWriter

public abstract class AbstractXmlWriter<T extends Interaction>
extends Object
implements InteractionWriter<T>

Abstract class for XML writer of interactions

Since:

11/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	AbstractXmlWriter(PsiXmlVersion version)	Constructor for AbstractXmlWriter.
	AbstractXmlWriter(PsiXmlVersion version, File file)	Constructor for AbstractXmlWriter.
	AbstractXmlWriter(PsiXmlVersion version, OutputStream output)	Constructor for AbstractXmlWriter.
	AbstractXmlWriter(PsiXmlVersion version, Writer writer)	Constructor for AbstractXmlWriter.
protected	AbstractXmlWriter(PsiXmlVersion version, XMLStreamWriter streamWriter, PsiXmlObjectCache elementCache)	Constructor for AbstractXmlWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	end()	Method to call when we reach the end
protected Source	extractSourceFromInteraction()	extractSourceFromInteraction.
void	flush()	Flushes the writer (commit or write on disk)
protected PsiXmlInteractionWriter<ModelledInteraction>	getComplexWriter()	Getter for the field complexWriter.
protected T	getCurrentInteraction()	Getter for the field currentInteraction.
protected Source	getCurrentSource()	Getter for the field currentSource.
protected PsiXmlObjectCache	getElementCache()	Getter for the field elementCache.
protected Iterator<? extends T>	getInteractionsIterator()	Getter for the field interactionsIterator.
protected PsiXmlInteractionWriter<T>	getInteractionWriter()	Getter for the field interactionWriter.
protected Set<Interaction>	getProcessedInteractions()	Getter for the field processedInteractions.
protected XMLStreamWriter	getStreamWriter()	Getter for the field streamWriter.
protected PsiXmlElementWriterFactory	getSubWritersFactory()	Getter for the field subWritersFactory.
protected PsiXmlVersion	getVersion()	Getter for the field version.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected abstract void	initialiseDefaultElementCache()	initialiseDefaultElementCache.
protected void	initialiseDefaultInteractionSet()	initialiseDefaultInteractionSet.
protected void	initialiseDefaultSource()	initialiseDefaultSource.
protected abstract void	initialiseOptionalWriters(PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlElementWriter<Interactor> interactorWriter)	initialiseOptionalWriters.
protected abstract void	initialiseSubWriters()	initialiseSubWriters.
protected void	initialiseSubWriters(boolean extended, boolean named, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType)	initialiseSubWriters.
protected boolean	isStarted()	isStarted.
protected ExtendedPsiXmlSource	newXmlSource(String shortName)
void	reset()	reset.
void	setAnnotationsWriter(PsiXmlElementWriter<Annotation> annotationsWriter)	Setter for the field annotationsWriter.
void	setComplexWriter(PsiXmlInteractionWriter<ModelledInteraction> complexWriter)	Setter for the field complexWriter.
protected void	setCurrentInteraction(T currentInteraction)	Setter for the field currentInteraction.
protected void	setCurrentSource(Source currentSource)	Setter for the field currentSource.
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.
void	setEntryAnnotations(Collection<Annotation> entryAnnotations)	Setter for the field entryAnnotations.
void	setInteractionSet(Set<Interaction> processedInteractions)	setInteractionSet.
protected void	setInteractionsIterator(Iterator<? extends T> interactionsIterator)	Setter for the field interactionsIterator.
protected void	setInteractionWriter(PsiXmlInteractionWriter<T> interactionWriter)	Setter for the field interactionWriter.
void	setSourceWriter(PsiXmlSourceWriter sourceWriter)	Setter for the field sourceWriter.
void	setStarted(boolean started)	Setter for the field started.
protected void	setSubWritersFactory(PsiXmlElementWriterFactory subWritersFactory)	Setter for the field subWritersFactory.
void	setVersion(PsiXmlVersion version)	Setter for the field version.
void	setWriteComplexesAsInteractors(boolean writeComplexesAsInteractors)	Setter for the field writeComplexesAsInteractors.
void	start()	Method to call before starting to write but after initialising the context
void	write(Collection<? extends T> interactions)	Writes a collection of Interaction objects
void	write(Iterator<? extends T> interactions)	Writes Interaction objects using iterator
void	write(T interaction)	Writes an interaction
protected void	writeComplex(ModelledInteraction modelled)	writeComplex.
protected boolean	writeComplexesAsInteractors()	writeComplexesAsInteractors.
protected void	writeEndEntry()	writeEndEntry.
protected void	writeEndEntryContent()	writeEndEntryContent.
protected void	writeEndInteractionList()	writeEndInteractionList.
protected void	writeEntryAttributes()	writeEntryAttributes.
protected void	writeEntrySetAttributes(String level, String version, String minorVersion, String namespaceURI, String schemaLocation)	writeEntrySetAttributes.
protected void	writeInteraction()	writeInteraction.
protected void	writeInteractionListContent()	writeInteractionListContent.
protected void	writeSource()	writeSource.
protected void	writeStartEntry()	writeStartEntry.
protected abstract void	writeStartEntryContent()	writeStartEntryContent.
protected void	writeStartInteractionList()	writeStartInteractionList.
protected void	writeSubComplexInEntry()	writeSubComplexInEntry.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractXmlWriter

public AbstractXmlWriter(PsiXmlVersion version)

Constructor for AbstractXmlWriter.

Parameters:

version - a PsiXmlVersion object.

AbstractXmlWriter

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

Constructor for AbstractXmlWriter.

Parameters:

version - a PsiXmlVersion object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

AbstractXmlWriter

public AbstractXmlWriter(PsiXmlVersion version,
                         OutputStream output)
                  throws XMLStreamException

Constructor for AbstractXmlWriter.

Parameters:

version - a PsiXmlVersion object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

AbstractXmlWriter

public AbstractXmlWriter(PsiXmlVersion version,
                         Writer writer)
                  throws XMLStreamException

Constructor for AbstractXmlWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a Writer object.

Throws:

XMLStreamException - if any.

AbstractXmlWriter

protected AbstractXmlWriter(PsiXmlVersion version,
                            XMLStreamWriter streamWriter,
                            PsiXmlObjectCache elementCache)

Constructor for AbstractXmlWriter.

Parameters:

version - a PsiXmlVersion 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>

Parameters:

options - : the options given by the user

end

public void end()
         throws MIIOException

Method to call when we reach the end

Specified by:

end in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - : if cannot end

start

public void start()
           throws MIIOException

Method to call before starting to write but after initialising the context

Specified by:

start in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if cannot start writing

writeEntrySetAttributes

protected void writeEntrySetAttributes(String level,
                                       String version,
                                       String minorVersion,
                                       String namespaceURI,
                                       String schemaLocation)
                                throws XMLStreamException

writeEntrySetAttributes.

Parameters:

level - a String object.

version - a String object.

minorVersion - a String object.

namespaceURI - a String object.

schemaLocation - a String object.

Throws:

XMLStreamException - if any.

write

public void write(T interaction)
           throws MIIOException

Writes an interaction

Specified by:

write in interface InteractionWriter<T extends Interaction>

Parameters:

interaction - : the interaction to write

Throws:

MIIOException - : if cannot write

write

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

Writes a collection of Interaction objects

Specified by:

write in interface InteractionWriter<T extends Interaction>

Parameters:

interactions - : the interactions to write

Throws:

MIIOException - : if cannot write

write

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

Writes Interaction objects using iterator

Specified by:

write in interface InteractionWriter<T extends Interaction>

Parameters:

interactions - : the iterator of interactions to write

Throws:

MIIOException - : if cannot write

flush

public void flush()
           throws MIIOException

Flushes the writer (commit or write on disk)

Specified by:

flush in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - : if cannot flush

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if any.

setWriteComplexesAsInteractors

public void setWriteComplexesAsInteractors(boolean writeComplexesAsInteractors)

Setter for the field writeComplexesAsInteractors.

Parameters:

writeComplexesAsInteractors - a boolean.

setInteractionSet

public void setInteractionSet(Set<Interaction> processedInteractions)

setInteractionSet.

Parameters:

processedInteractions - a Set object.

setSourceWriter

public void setSourceWriter(PsiXmlSourceWriter sourceWriter)

Setter for the field sourceWriter.

Parameters:

sourceWriter - a PsiXmlSourceWriter object.

setComplexWriter

public void setComplexWriter(PsiXmlInteractionWriter<ModelledInteraction> complexWriter)

Setter for the field complexWriter.

Parameters:

complexWriter - a PsiXmlInteractionWriter object.

setElementCache

public void setElementCache(PsiXmlObjectCache elementCache)

Setter for the field elementCache.

Parameters:

elementCache - a PsiXmlObjectCache object.

setStarted

public void setStarted(boolean started)

Setter for the field started.

Parameters:

started - a boolean.

setDefaultSource

public void setDefaultSource(Source defaultSource)

Setter for the field defaultSource.

Parameters:

defaultSource - a Source object.

setDefaultReleaseDate

public void setDefaultReleaseDate(XMLGregorianCalendar defaultReleaseDate)

Setter for the field defaultReleaseDate.

Parameters:

defaultReleaseDate - a XMLGregorianCalendar object.

setEntryAnnotations

public void setEntryAnnotations(Collection<Annotation> entryAnnotations)

Setter for the field entryAnnotations.

Parameters:

entryAnnotations - a Collection object.

setAnnotationsWriter

public void setAnnotationsWriter(PsiXmlElementWriter<Annotation> annotationsWriter)

Setter for the field annotationsWriter.

Parameters:

annotationsWriter - a PsiXmlElementWriter object.

setVersion

public void setVersion(PsiXmlVersion version)

Setter for the field version.

Parameters:

version - a PsiXmlVersion object.

getProcessedInteractions

protected Set<Interaction> getProcessedInteractions()

Getter for the field processedInteractions.

Returns:

a Set object.

writeEndEntryContent

protected void writeEndEntryContent()
                             throws XMLStreamException

writeEndEntryContent.

Throws:

XMLStreamException - if any.

writeEntryAttributes

protected void writeEntryAttributes()
                             throws XMLStreamException

writeEntryAttributes.

Throws:

XMLStreamException - if any.

writeInteractionListContent

protected void writeInteractionListContent()

writeInteractionListContent.

writeStartEntryContent

protected abstract void writeStartEntryContent()
                                        throws XMLStreamException

writeStartEntryContent.

Throws:

XMLStreamException - if any.

writeStartInteractionList

protected void writeStartInteractionList()
                                  throws XMLStreamException

writeStartInteractionList.

Throws:

XMLStreamException - if any.

writeEndInteractionList

protected void writeEndInteractionList()
                                throws XMLStreamException

writeEndInteractionList.

Throws:

XMLStreamException - if any.

writeInteraction

protected void writeInteraction()
                         throws XMLStreamException

writeInteraction.

Throws:

XMLStreamException - if any.

writeSubComplexInEntry

protected void writeSubComplexInEntry()
                               throws XMLStreamException

writeSubComplexInEntry.

Throws:

XMLStreamException - if any.

writeComplex

protected void writeComplex(ModelledInteraction modelled)

writeComplex.

Parameters:

modelled - a ModelledInteraction object.

extractSourceFromInteraction

protected Source extractSourceFromInteraction()

extractSourceFromInteraction.

Returns:

a Source object.

initialiseDefaultSource

protected void initialiseDefaultSource()

initialiseDefaultSource.

writeSource

protected void writeSource()
                    throws XMLStreamException

writeSource.

Throws:

XMLStreamException - if any.

writeStartEntry

protected void writeStartEntry()
                        throws XMLStreamException

writeStartEntry.

Throws:

XMLStreamException - if any.

writeEndEntry

protected void writeEndEntry()
                      throws XMLStreamException

writeEndEntry.

Throws:

XMLStreamException - if any.

initialiseSubWriters

protected void initialiseSubWriters(boolean extended,
                                    boolean named,
                                    PsiXmlType xmlType,
                                    InteractionCategory interactionCategory,
                                    ComplexType complexType)

initialiseSubWriters.

Parameters:

extended - a boolean.

named - a boolean.

xmlType - a PsiXmlType object.

interactionCategory - a InteractionCategory object.

complexType - a ComplexType object.

initialiseOptionalWriters

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

initialiseOptionalWriters.

Parameters:

experimentWriter - a PsiXmlExperimentWriter object.

availabilityWriter - a PsiXmlElementWriter object.

interactorWriter - a PsiXmlElementWriter object.

initialiseDefaultElementCache

protected abstract void initialiseDefaultElementCache()

initialiseDefaultElementCache.

getInteractionWriter

protected PsiXmlInteractionWriter<T> getInteractionWriter()

Getter for the field interactionWriter.

Returns:

a PsiXmlInteractionWriter object.

getComplexWriter

protected PsiXmlInteractionWriter<ModelledInteraction> getComplexWriter()

Getter for the field complexWriter.

Returns:

a PsiXmlInteractionWriter object.

getElementCache

protected PsiXmlObjectCache getElementCache()

Getter for the field elementCache.

Returns:

a PsiXmlObjectCache object.

setCurrentSource

protected void setCurrentSource(Source currentSource)

Setter for the field currentSource.

Parameters:

currentSource - a Source object.

getCurrentSource

protected Source getCurrentSource()

Getter for the field currentSource.

Returns:

a Source object.

getInteractionsIterator

protected Iterator<? extends T> getInteractionsIterator()

Getter for the field interactionsIterator.

Returns:

a Iterator object.

setInteractionsIterator

protected void setInteractionsIterator(Iterator<? extends T> interactionsIterator)

Setter for the field interactionsIterator.

Parameters:

interactionsIterator - a Iterator object.

setInteractionWriter

protected void setInteractionWriter(PsiXmlInteractionWriter<T> interactionWriter)

Setter for the field interactionWriter.

Parameters:

interactionWriter - a PsiXmlInteractionWriter object.

getStreamWriter

protected XMLStreamWriter getStreamWriter()

Getter for the field streamWriter.

Returns:

a XMLStreamWriter object.

getCurrentInteraction

protected T getCurrentInteraction()

Getter for the field currentInteraction.

Returns:

a T object.

setCurrentInteraction

protected void setCurrentInteraction(T currentInteraction)

Setter for the field currentInteraction.

Parameters:

currentInteraction - a T object.

isStarted

protected boolean isStarted()

isStarted.

Returns:

a boolean.

writeComplexesAsInteractors

protected boolean writeComplexesAsInteractors()

writeComplexesAsInteractors.

Returns:

a boolean.

initialiseDefaultInteractionSet

protected void initialiseDefaultInteractionSet()

initialiseDefaultInteractionSet.

getVersion

protected PsiXmlVersion getVersion()

Getter for the field version.

Returns:

a PsiXmlVersion object.

initialiseSubWriters

protected abstract void initialiseSubWriters()

initialiseSubWriters.

getSubWritersFactory

protected PsiXmlElementWriterFactory getSubWritersFactory()

Getter for the field subWritersFactory.

Returns:

a PsiXmlElementWriterFactory object.

setSubWritersFactory

protected void setSubWritersFactory(PsiXmlElementWriterFactory subWritersFactory)

Setter for the field subWritersFactory.

Parameters:

subWritersFactory - a PsiXmlElementWriterFactory object.

newXmlSource

protected ExtendedPsiXmlSource newXmlSource(String shortName)