Package psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30

Class AbstractXmlModelledParticipantWriter

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

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

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30.AbstractXmlModelledParticipantWriter

All Implemented Interfaces:

PsiXmlElementWriter<ModelledParticipant>, PsiXmlParticipantWriter<ModelledParticipant>

Direct Known Subclasses:

XmlModelledParticipantWriter, XmlModelledParticipantWriter

public abstract class AbstractXmlModelledParticipantWriter
extends AbstractXmlModelledParticipantWriter

Abstract class for XML 3.0 writer of modelled participant

Since:

14/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractXmlModelledParticipantWriter(XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for AbstractXmlModelledParticipantWriter.

Method Summary

Modifier and Type	Method	Description
PsiXmlElementWriter<ModelledParticipantCandidate>	getParticipantCandidateWriter()	Getter for the field participantCandidateWriter.
PsiXmlElementWriter<Stoichiometry>	getStoichiometryWriter()	Getter for the field stoichiometryWriter.
protected void	initialiseBiologicalRoleWriter()	initialiseBiologicalRoleWriter.
protected void	initialiseFeatureWriter()	initialiseFeatureWriter.
protected void	initialiseInteractorWriter()	initialiseInteractorWriter.
protected abstract void	initialiseParticipantCandidateWriter()	initialiseParticipantCandidateWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
void	setParticipantCandidateWriter(PsiXmlElementWriter<ModelledParticipantCandidate> participantCandidateWriter)	Setter for the field participantCandidateWriter.
void	setStoichiometryWriter(PsiXmlElementWriter<Stoichiometry> stoichiometryWriter)	Setter for the field stoichiometryWriter.
protected void	writeConfidences(ModelledParticipant object)	writeConfidences.
protected void	writeExperimentalInteractor(ModelledParticipant object)	writeExperimentalInteractor.
protected void	writeExperimentalPreparations(ModelledParticipant object)	writeExperimentalPreparations.
protected void	writeExperimentalRoles(ModelledParticipant object)	writeExperimentalRoles.
protected void	writeHostOrganisms(ModelledParticipant object)	writeHostOrganisms.
protected void	writeOtherAttributes(ModelledParticipant object, boolean writeAttributeList)	writeOtherAttributes.
protected void	writeParameters(ModelledParticipant object)	writeParameters.
protected void	writeParticipantIdentificationMethods(ModelledParticipant object, CvTerm method)	writeParticipantIdentificationMethods.
protected void	writeParticipantPool(ParticipantPool pool)	writeParticipantPool.
protected void	writeStoichiometry(ModelledParticipant object)	writeStoichiometry.

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlModelledParticipantWriter

writeMolecule

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlParticipantWriter

getAliasWriter, getAttributeWriter, getBiologicalRoleWriter, getFeatureWriter, getInteractorWriter, getObjectIndex, getStreamWriter, getVersion, getXrefWriter, setAliasWriter, setAttributeWriter, setBiologicalRoleWriter, setComplexAsInteractor, setFeatureWriter, setInteractorWriter, setXrefWriter, write, writeAttributes, writeBiologicalRole, writeComplexAsInteractor, writeFeatures, writeInteractor, writeMoleculeDescription, writeMoleculeRef, writeNames, writeParticipant, writeXref, writeXrefFromParticipantXrefs

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractXmlModelledParticipantWriter

public AbstractXmlModelledParticipantWriter(XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlModelledParticipantWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getStoichiometryWriter

public PsiXmlElementWriter<Stoichiometry> getStoichiometryWriter()

Getter for the field stoichiometryWriter.

Returns:

a PsiXmlElementWriter object.

setStoichiometryWriter

public void setStoichiometryWriter(PsiXmlElementWriter<Stoichiometry> stoichiometryWriter)

Setter for the field stoichiometryWriter.

Parameters:

stoichiometryWriter - a PsiXmlElementWriter object.

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Specified by:

initialiseXrefWriter in class AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

initialiseFeatureWriter

protected void initialiseFeatureWriter()

initialiseFeatureWriter.

Specified by:

initialiseFeatureWriter in class AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

writeStoichiometry

protected void writeStoichiometry(ModelledParticipant object)

writeStoichiometry.

Specified by:

writeStoichiometry in class AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

Parameters:

object - a ModelledParticipant object.

writeOtherAttributes

protected void writeOtherAttributes(ModelledParticipant object,
                                    boolean writeAttributeList)
                             throws XMLStreamException

writeOtherAttributes.

Specified by:

writeOtherAttributes in class AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

Parameters:

object - a P object.

writeAttributeList - a boolean.

Throws:

XMLStreamException - if any.

initialiseBiologicalRoleWriter

protected void initialiseBiologicalRoleWriter()

initialiseBiologicalRoleWriter.

Specified by:

initialiseBiologicalRoleWriter in class AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

initialiseInteractorWriter

protected void initialiseInteractorWriter()

initialiseInteractorWriter.

Specified by:

initialiseInteractorWriter in class AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

writeExperimentalPreparations

protected void writeExperimentalPreparations(ModelledParticipant object)

writeExperimentalPreparations.

Overrides:

writeExperimentalPreparations in class AbstractXmlModelledParticipantWriter

Parameters:

object - a P object.

writeExperimentalRoles

protected void writeExperimentalRoles(ModelledParticipant object)

writeExperimentalRoles.

Overrides:

writeExperimentalRoles in class AbstractXmlModelledParticipantWriter

Parameters:

object - a P object.

writeParticipantIdentificationMethods

protected void writeParticipantIdentificationMethods(ModelledParticipant object,
                                                     CvTerm method)

writeParticipantIdentificationMethods.

Overrides:

writeParticipantIdentificationMethods in class AbstractXmlModelledParticipantWriter

Parameters:

object - a P object.

method - a CvTerm object.

writeExperimentalInteractor

protected void writeExperimentalInteractor(ModelledParticipant object)

writeExperimentalInteractor.

Overrides:

writeExperimentalInteractor in class AbstractXmlModelledParticipantWriter

Parameters:

object - a P object.

writeHostOrganisms

protected void writeHostOrganisms(ModelledParticipant object)

writeHostOrganisms.

Overrides:

writeHostOrganisms in class AbstractXmlModelledParticipantWriter

Parameters:

object - a P object.

writeConfidences

protected void writeConfidences(ModelledParticipant object)

writeConfidences.

Overrides:

writeConfidences in class AbstractXmlModelledParticipantWriter

Parameters:

object - a P object.

writeParameters

protected void writeParameters(ModelledParticipant object)

writeParameters.

Overrides:

writeParameters in class AbstractXmlModelledParticipantWriter

Parameters:

object - a P object.

getParticipantCandidateWriter

public PsiXmlElementWriter<ModelledParticipantCandidate> getParticipantCandidateWriter()

Getter for the field participantCandidateWriter.

Returns:

a PsiXmlElementWriter object.

initialiseParticipantCandidateWriter

protected abstract void initialiseParticipantCandidateWriter()

initialiseParticipantCandidateWriter.

setParticipantCandidateWriter

public void setParticipantCandidateWriter(PsiXmlElementWriter<ModelledParticipantCandidate> participantCandidateWriter)

Setter for the field participantCandidateWriter.

Parameters:

participantCandidateWriter - a PsiXmlElementWriter object.

writeParticipantPool

protected void writeParticipantPool(ParticipantPool pool)
                             throws XMLStreamException

writeParticipantPool.

Specified by:

writeParticipantPool in class AbstractXmlParticipantWriter<ModelledParticipant,ModelledFeature>

Parameters:

pool - a ParticipantPool object.

Throws:

XMLStreamException - if any.