Package psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts

Class AbstractXmlInteractionWriter<T extends Interaction,P extends Participant>

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlInteractionWriter<T,P>

All Implemented Interfaces:

PsiXmlElementWriter<T>, PsiXmlInteractionWriter<T>

Direct Known Subclasses:

AbstractXmlInteractionEvidenceWriter, AbstractXmlInteractionWriter, AbstractXmlModelledInteractionWriter

public abstract class AbstractXmlInteractionWriter<T extends Interaction,P extends Participant>
extends Object
implements PsiXmlInteractionWriter<T>

Abstract writer of interaction

Since:

12/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractXmlInteractionWriter(PsiXmlVersion version, XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for AbstractXmlInteractionWriter.

Method Summary

Modifier and Type	Method	Description
protected Collection<Set<Feature>>	collectInferredInteractionsFrom(T object)	collectInferredInteractionsFrom.
Experiment	extractDefaultExperimentFrom(T interaction)	extractDefaultExperimentFrom.
PsiXmlElementWriter<Annotation>	getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Checksum>	getChecksumWriter()	Getter for the field checksumWriter.
Experiment	getDefaultExperiment()	Getter for the field defaultExperiment.
PsiXmlExperimentWriter	getExperimentWriter()	Getter for the field experimentWriter.
PsiXmlElementWriter<Set<Feature>>	getInferredInteractionWriter()	Getter for the field inferredInteractionWriter.
PsiXmlVariableNameWriter<CvTerm>	getInteractionTypeWriter()	Getter for the field interactionTypeWriter.
protected PsiXmlObjectCache	getObjectIndex()	Getter for the field objectIndex.
PsiXmlParticipantWriter<P>	getParticipantWriter()	Getter for the field participantWriter.
protected XMLStreamWriter	getStreamWriter()	Getter for the field streamWriter.
protected PsiXmlVersion	getVersion()
PsiXmlXrefWriter	getXrefWriter()	Getter for the field xrefWriter.
protected void	initialiseDefaultExperiment()	initialiseDefaultExperiment.
protected abstract void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected abstract void	initialiseInferredInteractionWriter()	initialiseInferredInteractionWriter.
protected abstract void	initialiseInteractionTypeWriter()	initialiseInteractionTypeWriter.
protected abstract void	initialiseParticipantWriter()	initialiseParticipantWriter.
protected abstract void	initialiseXrefWriter()	initialiseXrefWriter.
protected ExtendedPsiXmlExperiment	newExperiment(Publication publication)
protected Publication	newPublication(String pubmed)
protected Publication	newPublication(String title, String journal, Date publicationDate)
protected CvTerm	newXmlCvTerm(String shortName, CvTerm database, String id, CvTerm qualifier)
void	setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	setChecksumWriter(PsiXmlElementWriter<Checksum> checksumWriter)	Setter for the field checksumWriter.
void	setComplexAsInteractor(boolean complexAsInteractor)	Sets the property of the writer to write a complex as an interactor or as an interaction
void	setDefaultExperiment(Experiment defaultExperiment)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	setExperimentWriter(PsiXmlExperimentWriter experimentWriter)	Setter for the field experimentWriter.
void	setInferredInteractionWriter(PsiXmlElementWriter<Set<Feature>> inferredInteractionWriter)	Setter for the field inferredInteractionWriter.
void	setInteractionTypeWriter(PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter)	Setter for the field interactionTypeWriter.
void	setParticipantWriter(PsiXmlParticipantWriter<P> participantWriter)	Setter for the field participantWriter.
void	setXrefWriter(PsiXmlXrefWriter xrefWriter)	Setter for the field xrefWriter.
void	write(T object)	write.
protected void	writeAttribute(String name, String nameAc)	writeAttribute.
protected void	writeAttributes(T object)	writeAttributes.
protected abstract void	writeAvailability(T object)	writeAvailability.
boolean	writeComplexAsInteractor()	writeComplexAsInteractor.
protected abstract void	writeConfidences(T object)	writeConfidences.
protected CvTerm	writeExperimentDescription()	writeExperimentDescription.
protected CvTerm	writeExperimentRef()	writeExperimentRef.
protected abstract CvTerm	writeExperiments(T object)	writeExperiments.
protected abstract void	writeInferredInteractions(T object)	writeInferredInteractions.
protected void	writeInteractionType(T object)	writeInteractionType.
protected void	writeIntraMolecular(T object)	writeIntraMolecular.
protected abstract void	writeModelled(T object)	writeModelled.
protected void	writeNames(T object)	writeNames.
protected abstract void	writeNegative(T object)	writeNegative.
protected abstract void	writeOtherAttributes(T object)	writeOtherAttributes.
protected abstract void	writeOtherProperties(T object)	writeOtherProperties.
protected abstract void	writeParameters(T object)	writeParameters.
protected void	writeParticipants(T object, CvTerm method)	writeParticipants.
protected abstract void	writeStartInteraction()	writeStartInteraction.
protected void	writeXref(T object)	writeXref.
protected void	writeXrefFromInteractionIdentifiers(T object)	writeXrefFromInteractionIdentifiers.
protected void	writeXrefFromInteractionXrefs(T object)	writeXrefFromInteractionXrefs.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractXmlInteractionWriter

public AbstractXmlInteractionWriter(PsiXmlVersion version,
                                    XMLStreamWriter writer,
                                    PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlInteractionWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getParticipantWriter

public PsiXmlParticipantWriter<P> getParticipantWriter()

Getter for the field participantWriter.

Returns:

a PsiXmlParticipantWriter object.

initialiseParticipantWriter

protected abstract void initialiseParticipantWriter()

initialiseParticipantWriter.

setParticipantWriter

public void setParticipantWriter(PsiXmlParticipantWriter<P> participantWriter)

Setter for the field participantWriter.

Parameters:

participantWriter - a PsiXmlParticipantWriter object.

getXrefWriter

public PsiXmlXrefWriter getXrefWriter()

Getter for the field xrefWriter.

Returns:

a PsiXmlXrefWriter object.

initialiseXrefWriter

protected abstract void initialiseXrefWriter()

initialiseXrefWriter.

setXrefWriter

public void setXrefWriter(PsiXmlXrefWriter xrefWriter)

Setter for the field xrefWriter.

Parameters:

xrefWriter - a PsiXmlXrefWriter object.

setInteractionTypeWriter

public void setInteractionTypeWriter(PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter)

Setter for the field interactionTypeWriter.

Parameters:

interactionTypeWriter - a PsiXmlVariableNameWriter object.

setAttributeWriter

public void setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)

Setter for the field attributeWriter.

Parameters:

attributeWriter - a PsiXmlElementWriter object.

getInferredInteractionWriter

public PsiXmlElementWriter<Set<Feature>> getInferredInteractionWriter()

Getter for the field inferredInteractionWriter.

Returns:

a PsiXmlElementWriter object.

initialiseInferredInteractionWriter

protected abstract void initialiseInferredInteractionWriter()

initialiseInferredInteractionWriter.

setInferredInteractionWriter

public void setInferredInteractionWriter(PsiXmlElementWriter<Set<Feature>> inferredInteractionWriter)

Setter for the field inferredInteractionWriter.

Parameters:

inferredInteractionWriter - a PsiXmlElementWriter object.

setExperimentWriter

public void setExperimentWriter(PsiXmlExperimentWriter experimentWriter)

Setter for the field experimentWriter.

Parameters:

experimentWriter - a PsiXmlExperimentWriter object.

setChecksumWriter

public void setChecksumWriter(PsiXmlElementWriter<Checksum> checksumWriter)

Setter for the field checksumWriter.

Parameters:

checksumWriter - a PsiXmlElementWriter object.

getExperimentWriter

public PsiXmlExperimentWriter getExperimentWriter()

Getter for the field experimentWriter.

Returns:

a PsiXmlExperimentWriter object.

initialiseExperimentWriter

protected abstract void initialiseExperimentWriter()

initialiseExperimentWriter.

getChecksumWriter

public PsiXmlElementWriter<Checksum> getChecksumWriter()

Getter for the field checksumWriter.

Returns:

a PsiXmlElementWriter object.

getInteractionTypeWriter

public PsiXmlVariableNameWriter<CvTerm> getInteractionTypeWriter()

Getter for the field interactionTypeWriter.

Returns:

a PsiXmlVariableNameWriter object.

initialiseInteractionTypeWriter

protected abstract void initialiseInteractionTypeWriter()

initialiseInteractionTypeWriter.

getAttributeWriter

public PsiXmlElementWriter<Annotation> getAttributeWriter()

Getter for the field attributeWriter.

Returns:

a PsiXmlElementWriter object.

write

public void write(T object)
           throws MIIOException

write.

Specified by:

write in interface PsiXmlElementWriter<T extends Interaction>

Parameters:

object - a T object.

Throws:

MIIOException - if any.

writeOtherProperties

protected abstract void writeOtherProperties(T object)
                                      throws XMLStreamException

writeOtherProperties.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeStartInteraction

protected abstract void writeStartInteraction()
                                       throws XMLStreamException

writeStartInteraction.

Throws:

XMLStreamException - if any.

getDefaultExperiment

public Experiment getDefaultExperiment()

Getter for the field defaultExperiment.

Specified by:

getDefaultExperiment in interface PsiXmlInteractionWriter<T extends Interaction>

Returns:

a Experiment object.

setDefaultExperiment

public void setDefaultExperiment(Experiment defaultExperiment)

Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment

Specified by:

setDefaultExperiment in interface PsiXmlInteractionWriter<T extends Interaction>

Parameters:

defaultExperiment - : default experiment

extractDefaultExperimentFrom

public Experiment extractDefaultExperimentFrom(T interaction)

extractDefaultExperimentFrom.

Specified by:

extractDefaultExperimentFrom in interface PsiXmlInteractionWriter<T extends Interaction>

Parameters:

interaction - a T object.

Returns:

the default experiment for this interaction

writeComplexAsInteractor

public boolean writeComplexAsInteractor()

writeComplexAsInteractor.

Specified by:

writeComplexAsInteractor in interface PsiXmlInteractionWriter<T extends Interaction>

Returns:

true if the participant writer will write a complex as an interactor

setComplexAsInteractor

public void setComplexAsInteractor(boolean complexAsInteractor)

Sets the property of the writer to write a complex as an interactor or as an interaction

Specified by:

setComplexAsInteractor in interface PsiXmlInteractionWriter<T extends Interaction>

Parameters:

complexAsInteractor - a boolean.

writeAttributes

protected void writeAttributes(T object)
                        throws XMLStreamException

writeAttributes.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeInteractionType

protected void writeInteractionType(T object)
                             throws XMLStreamException

writeInteractionType.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeInferredInteractions

protected abstract void writeInferredInteractions(T object)
                                           throws XMLStreamException

writeInferredInteractions.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeParticipants

protected void writeParticipants(T object,
                                 CvTerm method)
                          throws XMLStreamException

writeParticipants.

Parameters:

object - a T object.

method - a CvTerm object.

Throws:

XMLStreamException - if any.

writeNames

protected void writeNames(T object)
                   throws XMLStreamException

writeNames.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeAvailability

protected abstract void writeAvailability(T object)
                                   throws XMLStreamException

writeAvailability.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeExperiments

protected abstract CvTerm writeExperiments(T object)
                                    throws XMLStreamException

writeExperiments.

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeOtherAttributes

protected abstract void writeOtherAttributes(T object)
                                      throws XMLStreamException

writeOtherAttributes.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeIntraMolecular

protected void writeIntraMolecular(T object)
                            throws XMLStreamException

writeIntraMolecular.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeModelled

protected abstract void writeModelled(T object)
                               throws XMLStreamException

writeModelled.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeXref

protected void writeXref(T object)
                  throws XMLStreamException

writeXref.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeXrefFromInteractionXrefs

protected void writeXrefFromInteractionXrefs(T object)
                                      throws XMLStreamException

writeXrefFromInteractionXrefs.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeXrefFromInteractionIdentifiers

protected void writeXrefFromInteractionIdentifiers(T object)
                                            throws XMLStreamException

writeXrefFromInteractionIdentifiers.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

getStreamWriter

protected XMLStreamWriter getStreamWriter()

Getter for the field streamWriter.

Returns:

a XMLStreamWriter object.

getObjectIndex

protected PsiXmlObjectCache getObjectIndex()

Getter for the field objectIndex.

Returns:

a PsiXmlObjectCache object.

writeParameters

protected abstract void writeParameters(T object)
                                 throws XMLStreamException

writeParameters.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeConfidences

protected abstract void writeConfidences(T object)
                                  throws XMLStreamException

writeConfidences.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeNegative

protected abstract void writeNegative(T object)
                               throws XMLStreamException

writeNegative.

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeExperimentRef

protected CvTerm writeExperimentRef()
                             throws XMLStreamException

writeExperimentRef.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperimentDescription

protected CvTerm writeExperimentDescription()
                                     throws XMLStreamException

writeExperimentDescription.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

initialiseDefaultExperiment

protected void initialiseDefaultExperiment()

initialiseDefaultExperiment.

writeAttribute

protected void writeAttribute(String name,
                              String nameAc)
                       throws XMLStreamException

writeAttribute.

Parameters:

name - a String object.

nameAc - a String object.

Throws:

XMLStreamException - if any.

collectInferredInteractionsFrom

protected Collection<Set<Feature>> collectInferredInteractionsFrom(T object)

collectInferredInteractionsFrom.

Parameters:

object - a T object.

Returns:

a Collection object.

getVersion

protected PsiXmlVersion getVersion()

newExperiment

protected ExtendedPsiXmlExperiment newExperiment(Publication publication)

newPublication

protected Publication newPublication(String title,
                                     String journal,
                                     Date publicationDate)

newPublication

protected Publication newPublication(String pubmed)

newXmlCvTerm

protected CvTerm newXmlCvTerm(String shortName,
                              CvTerm database,
                              String id,
                              CvTerm qualifier)