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

Class AbstractXmlParticipantWriter<P extends Participant,F extends Feature>

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlParticipantWriter<P,F>

All Implemented Interfaces:

PsiXmlElementWriter<P>, PsiXmlParticipantWriter<P>

Direct Known Subclasses:

AbstractXmlModelledParticipantWriter, AbstractXmlParticipantEvidenceWriter, AbstractXmlParticipantWriter

public abstract class AbstractXmlParticipantWriter<P extends Participant,F extends Feature>
extends Object
implements PsiXmlParticipantWriter<P>

Abstract Xml writer for participant

Since:

12/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Annotation>	getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlVariableNameWriter<CvTerm>	getBiologicalRoleWriter()	Getter for the field biologicalRoleWriter.
PsiXmlElementWriter<F>	getFeatureWriter()	Getter for the field featureWriter.
PsiXmlElementWriter<Interactor>	getInteractorWriter()	Getter for the field interactorWriter.
protected PsiXmlObjectCache	getObjectIndex()	Getter for the field objectIndex.
protected XMLStreamWriter	getStreamWriter()	Getter for the field streamWriter.
protected PsiXmlVersion	getVersion()
PsiXmlXrefWriter	getXrefWriter()	Getter for the field xrefWriter.
protected abstract void	initialiseBiologicalRoleWriter()	initialiseBiologicalRoleWriter.
protected abstract void	initialiseFeatureWriter()	initialiseFeatureWriter.
protected abstract void	initialiseInteractorWriter()	initialiseInteractorWriter.
protected abstract void	initialiseXrefWriter()	initialiseXrefWriter.
void	setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	setBiologicalRoleWriter(PsiXmlVariableNameWriter<CvTerm> biologicalRoleWriter)	Setter for the field biologicalRoleWriter.
void	setComplexAsInteractor(boolean complexAsInteractor)	Sets the property of the writer to write a complex as an interactor or as an interaction
void	setFeatureWriter(PsiXmlElementWriter<F> featureWriter)	Setter for the field featureWriter.
void	setInteractorWriter(PsiXmlElementWriter<Interactor> interactorWriter)	Setter for the field interactorWriter.
void	setXrefWriter(PsiXmlXrefWriter xrefWriter)	Setter for the field xrefWriter.
void	write(P object)	write.
protected void	writeAttributes(P object)	writeAttributes.
protected void	writeBiologicalRole(P object)	writeBiologicalRole.
boolean	writeComplexAsInteractor()	writeComplexAsInteractor.
protected abstract void	writeConfidences(P object)	writeConfidences.
protected abstract void	writeExperimentalInteractor(P object)	writeExperimentalInteractor.
protected abstract void	writeExperimentalPreparations(P object)	writeExperimentalPreparations.
protected abstract void	writeExperimentalRoles(P object)	writeExperimentalRoles.
protected void	writeFeatures(P object)	writeFeatures.
protected abstract void	writeHostOrganisms(P object)	writeHostOrganisms.
protected void	writeInteractor(P object)	writeInteractor.
protected abstract void	writeMolecule(Interactor interactor)	writeMolecule.
protected void	writeMoleculeDescription(Interactor interactor)	writeMoleculeDescription.
protected void	writeMoleculeRef(Interactor interactor)	writeMoleculeRef.
protected void	writeNames(P object)	writeNames.
protected abstract void	writeOtherAttributes(P object, boolean writeAttributeList)	writeOtherAttributes.
protected abstract void	writeParameters(P object)	writeParameters.
void	writeParticipant(P object, CvTerm detectionMethod)	writeParticipant.
protected abstract void	writeParticipantIdentificationMethods(P object, CvTerm method)	writeParticipantIdentificationMethods.
protected abstract void	writeParticipantPool(ParticipantPool pool)	writeParticipantPool.
protected abstract void	writeStoichiometry(P object)	writeStoichiometry.
protected void	writeXref(P object)	writeXref.
protected void	writeXrefFromParticipantXrefs(P object)	writeXrefFromParticipantXrefs.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractXmlParticipantWriter

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

Constructor for AbstractXmlParticipantWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getAliasWriter

public PsiXmlElementWriter<Alias> getAliasWriter()

Getter for the field aliasWriter.

Returns:

a PsiXmlElementWriter object.

setAliasWriter

public void setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)

Setter for the field aliasWriter.

Parameters:

aliasWriter - a PsiXmlElementWriter 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.

getBiologicalRoleWriter

public PsiXmlVariableNameWriter<CvTerm> getBiologicalRoleWriter()

Getter for the field biologicalRoleWriter.

Returns:

a PsiXmlVariableNameWriter object.

initialiseBiologicalRoleWriter

protected abstract void initialiseBiologicalRoleWriter()

initialiseBiologicalRoleWriter.

setBiologicalRoleWriter

public void setBiologicalRoleWriter(PsiXmlVariableNameWriter<CvTerm> biologicalRoleWriter)

Setter for the field biologicalRoleWriter.

Parameters:

biologicalRoleWriter - a PsiXmlVariableNameWriter object.

getAttributeWriter

public PsiXmlElementWriter<Annotation> getAttributeWriter()

Getter for the field attributeWriter.

Returns:

a PsiXmlElementWriter object.

setAttributeWriter

public void setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)

Setter for the field attributeWriter.

Parameters:

attributeWriter - a PsiXmlElementWriter object.

getInteractorWriter

public PsiXmlElementWriter<Interactor> getInteractorWriter()

Getter for the field interactorWriter.

Returns:

a PsiXmlElementWriter object.

initialiseInteractorWriter

protected abstract void initialiseInteractorWriter()

initialiseInteractorWriter.

setInteractorWriter

public void setInteractorWriter(PsiXmlElementWriter<Interactor> interactorWriter)

Setter for the field interactorWriter.

Parameters:

interactorWriter - a PsiXmlElementWriter object.

getFeatureWriter

public PsiXmlElementWriter<F> getFeatureWriter()

Getter for the field featureWriter.

Returns:

a PsiXmlElementWriter object.

initialiseFeatureWriter

protected abstract void initialiseFeatureWriter()

initialiseFeatureWriter.

setFeatureWriter

public void setFeatureWriter(PsiXmlElementWriter<F> featureWriter)

Setter for the field featureWriter.

Parameters:

featureWriter - a PsiXmlElementWriter object.

write

public void write(P object)
           throws MIIOException

write.

Specified by:

write in interface PsiXmlElementWriter<P extends Participant>

Parameters:

object - a T object.

Throws:

MIIOException - if any.

writeParticipant

public void writeParticipant(P object,
                             CvTerm detectionMethod)
                      throws MIIOException

writeParticipant.

Specified by:

writeParticipant in interface PsiXmlParticipantWriter<P extends Participant>

Parameters:

object - : participant to write

detectionMethod - : the experiment participant identification method which can be overridden by the participant

Throws:

MIIOException - if any.

writeComplexAsInteractor

public boolean writeComplexAsInteractor()

writeComplexAsInteractor.

Specified by:

writeComplexAsInteractor in interface PsiXmlParticipantWriter<P extends Participant>

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 PsiXmlParticipantWriter<P extends Participant>

Parameters:

complexAsInteractor - a boolean.

writeStoichiometry

protected abstract void writeStoichiometry(P object)

writeStoichiometry.

Parameters:

object - a P object.

writeOtherAttributes

protected abstract void writeOtherAttributes(P object,
                                             boolean writeAttributeList)
                                      throws XMLStreamException

writeOtherAttributes.

Parameters:

object - a P object.

writeAttributeList - a boolean.

Throws:

XMLStreamException - if any.

writeAttributes

protected void writeAttributes(P object)
                        throws XMLStreamException

writeAttributes.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeFeatures

protected void writeFeatures(P object)
                      throws XMLStreamException

writeFeatures.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeNames

protected void writeNames(P object)
                   throws XMLStreamException

writeNames.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeBiologicalRole

protected void writeBiologicalRole(P object)
                            throws XMLStreamException

writeBiologicalRole.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeInteractor

protected void writeInteractor(P object)
                        throws XMLStreamException

writeInteractor.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeParticipantPool

protected abstract void writeParticipantPool(ParticipantPool pool)
                                      throws XMLStreamException

writeParticipantPool.

Parameters:

pool - a ParticipantPool object.

Throws:

XMLStreamException - if any.

writeMolecule

protected abstract void writeMolecule(Interactor interactor)
                               throws XMLStreamException

writeMolecule.

Parameters:

interactor - a Interactor object.

Throws:

XMLStreamException - if any.

writeExperimentalPreparations

protected abstract void writeExperimentalPreparations(P object)
                                               throws XMLStreamException

writeExperimentalPreparations.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeExperimentalRoles

protected abstract void writeExperimentalRoles(P object)
                                        throws XMLStreamException

writeExperimentalRoles.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeParticipantIdentificationMethods

protected abstract void writeParticipantIdentificationMethods(P object,
                                                              CvTerm method)
                                                       throws XMLStreamException

writeParticipantIdentificationMethods.

Parameters:

object - a P object.

method - a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperimentalInteractor

protected abstract void writeExperimentalInteractor(P object)
                                             throws XMLStreamException

writeExperimentalInteractor.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeHostOrganisms

protected abstract void writeHostOrganisms(P object)
                                    throws XMLStreamException

writeHostOrganisms.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeConfidences

protected abstract void writeConfidences(P object)
                                  throws XMLStreamException

writeConfidences.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeParameters

protected abstract void writeParameters(P object)
                                 throws XMLStreamException

writeParameters.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeXref

protected void writeXref(P object)
                  throws XMLStreamException

writeXref.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeXrefFromParticipantXrefs

protected void writeXrefFromParticipantXrefs(P object)
                                      throws XMLStreamException

writeXrefFromParticipantXrefs.

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeMoleculeRef

protected void writeMoleculeRef(Interactor interactor)
                         throws XMLStreamException

writeMoleculeRef.

Parameters:

interactor - a Interactor object.

Throws:

XMLStreamException - if any.

writeMoleculeDescription

protected void writeMoleculeDescription(Interactor interactor)
                                 throws XMLStreamException

writeMoleculeDescription.

Parameters:

interactor - a Interactor 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.

getVersion

protected PsiXmlVersion getVersion()