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

Class AbstractExpandedXmlMixWriter<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.expanded.AbstractExpandedXmlWriter<I>

psidev.psi.mi.jami.xml.io.writer.expanded.AbstractExpandedXmlMixWriter<I,M,E>

All Implemented Interfaces:

InteractionWriter<I>

Direct Known Subclasses:

ExpandedXmlBinaryWriter, ExpandedXmlBinaryWriter, ExpandedXmlNamedBinaryWriter, ExpandedXmlNamedWriter, ExpandedXmlWriter, ExpandedXmlWriter

public abstract class AbstractExpandedXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence>
extends AbstractExpandedXmlWriter<I>

Abstract class for an expanded PSI-XML writer of mixed interactions

Since:

20/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	flush()	Flushes the writer (commit or write on disk)
protected AbstractExpandedXmlWriter<E>	getEvidenceWriter()	Getter for the field evidenceWriter.
protected AbstractExpandedXmlWriter<I>	getLightWriter()	Getter for the field lightWriter.
protected AbstractExpandedXmlWriter<M>	getModelledWriter()	Getter for the field modelledWriter.
protected abstract void	initialiseDelegateWriters()	initialiseDelegateWriters.
protected void	initialiseSubWriters()	initialiseSubWriters.
void	reset()	reset.
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(AbstractExpandedXmlWriter<E> evidenceWriter)	Setter for the field evidenceWriter.
void	setInteractionSet(Set<Interaction> processedInteractions)	setInteractionSet.
protected void	setLightWriter(AbstractExpandedXmlWriter<I> lightWriter)	Setter for the field lightWriter.
protected void	setModelledWriter(AbstractExpandedXmlWriter<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.expanded.AbstractExpandedXmlWriter

getInteractionType, initialiseDefaultElementCache, initialiseOptionalWriters, writeComplex, writeInteraction, 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, initialiseContext, initialiseDefaultInteractionSet, initialiseDefaultSource, initialiseSubWriters, isStarted, newXmlSource, setAnnotationsWriter, setCurrentInteraction, setCurrentSource, setEntryAnnotations, setInteractionsIterator, setInteractionWriter, setStarted, setSubWritersFactory, start, writeComplexesAsInteractors, writeEndEntry, writeEndEntryContent, writeEndInteractionList, writeEntryAttributes, writeEntrySetAttributes, 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

AbstractExpandedXmlMixWriter

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

Constructor for AbstractExpandedXmlMixWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

AbstractExpandedXmlMixWriter

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

Constructor for AbstractExpandedXmlMixWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

file - a File object.

Throws:

IOException - if any.

XMLStreamException - if any.

AbstractExpandedXmlMixWriter

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

Constructor for AbstractExpandedXmlMixWriter.

Parameters:

version - a PsiXmlVersion object.

type - a Class object.

output - a OutputStream object.

Throws:

XMLStreamException - if any.

AbstractExpandedXmlMixWriter

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

Constructor for AbstractExpandedXmlMixWriter.

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 AbstractXmlWriter<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 AbstractXmlWriter<I extends Interaction>

Throws:

MIIOException - if any.

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.

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.

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.

setVersion

public void setVersion(PsiXmlVersion version)

Setter for the field version.

Overrides:

setVersion in class AbstractXmlWriter<I extends Interaction>

Parameters:

version - a PsiXmlVersion object.

getEvidenceWriter

protected AbstractExpandedXmlWriter<E> getEvidenceWriter()

Getter for the field evidenceWriter.

Returns:

a AbstractExpandedXmlWriter object.

setEvidenceWriter

protected void setEvidenceWriter(AbstractExpandedXmlWriter<E> evidenceWriter)

Setter for the field evidenceWriter.

Parameters:

evidenceWriter - a AbstractExpandedXmlWriter object.

getModelledWriter

protected AbstractExpandedXmlWriter<M> getModelledWriter()

Getter for the field modelledWriter.

Returns:

a AbstractExpandedXmlWriter object.

setModelledWriter

protected void setModelledWriter(AbstractExpandedXmlWriter<M> modelledWriter)

Setter for the field modelledWriter.

Parameters:

modelledWriter - a AbstractExpandedXmlWriter object.

getLightWriter

protected AbstractExpandedXmlWriter<I> getLightWriter()

Getter for the field lightWriter.

Returns:

a AbstractExpandedXmlWriter object.

setLightWriter

protected void setLightWriter(AbstractExpandedXmlWriter<I> lightWriter)

Setter for the field lightWriter.

Parameters:

lightWriter - a AbstractExpandedXmlWriter object.

initialiseDelegateWriters

protected abstract void initialiseDelegateWriters()

initialiseDelegateWriters.