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

Class AbstractXmlParticipantEvidenceWriter

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

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

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

All Implemented Interfaces:

PsiXmlElementWriter<ParticipantEvidence>, PsiXmlParticipantWriter<ParticipantEvidence>

Direct Known Subclasses:

XmlNamedParticipantEvidenceWriter, XmlParticipantEvidenceWriter, XmlParticipantEvidenceWriter, XmlParticipantEvidenceWriter, XmlParticipantEvidenceWriter

public abstract class AbstractXmlParticipantEvidenceWriter
extends AbstractXmlParticipantEvidenceWriter

Abstract class for XML 3.0 writer of participant evidences

Since:

14/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
PsiXmlElementWriter<ExperimentalParticipantCandidate>	getParticipantCandidateWriter()	Getter for the field participantCandidateWriter.
PsiXmlElementWriter<Stoichiometry>	getStoichiometryWriter()	Getter for the field stoichiometryWriter.
protected void	initialiseBiologicalRoleWriter()	initialiseBiologicalRoleWriter.
protected void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseCvWriter()	initialiseCvWriter.
protected void	initialiseFeatureWriter()	initialiseFeatureWriter.
protected void	initialiseHostOrganismWriter()	initialiseHostOrganismWriter.
protected void	initialiseInteractorWriter()	initialiseInteractorWriter.
protected void	initialiseParameterWriter()	initialiseParameterWriter.
protected abstract void	initialiseParticipantCandidateWriter()	initialiseParticipantCandidateWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
void	setParticipantCandidateWriter(PsiXmlElementWriter<ExperimentalParticipantCandidate> participantCandidateWriter)	Setter for the field participantCandidateWriter.
void	setStoichiometryWriter(PsiXmlElementWriter<Stoichiometry> stoichiometryWriter)	Setter for the field stoichiometryWriter.
protected void	writeOtherAttributes(ParticipantEvidence object, boolean writeAttributeList)	writeOtherAttributes.
protected void	writeParticipantPool(ParticipantPool pool)	writeParticipantPool.
protected void	writeStoichiometry(ParticipantEvidence object)	writeStoichiometry.

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

getConfidenceWriter, getExperimentalCvWriter, getHostOrganismWriter, getParameterWriter, setConfidenceWriter, setExperimentalCvWriter, setHostOrganismWriter, setParameterWriter, writeConfidences, writeExperimentalInteractor, writeExperimentalPreparations, writeExperimentalRoles, writeHostOrganisms, writeParameters, writeParticipantIdentificationMethods

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, writeMolecule, 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

AbstractXmlParticipantEvidenceWriter

public AbstractXmlParticipantEvidenceWriter(XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlParticipantEvidenceWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Specified by:

initialiseXrefWriter in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

initialiseFeatureWriter

protected void initialiseFeatureWriter()

initialiseFeatureWriter.

Specified by:

initialiseFeatureWriter in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

initialiseConfidenceWriter

protected void initialiseConfidenceWriter()

initialiseConfidenceWriter.

Specified by:

initialiseConfidenceWriter in class AbstractXmlParticipantEvidenceWriter

initialiseHostOrganismWriter

protected void initialiseHostOrganismWriter()

initialiseHostOrganismWriter.

Specified by:

initialiseHostOrganismWriter in class AbstractXmlParticipantEvidenceWriter

initialiseParameterWriter

protected void initialiseParameterWriter()

initialiseParameterWriter.

Specified by:

initialiseParameterWriter in class AbstractXmlParticipantEvidenceWriter

initialiseCvWriter

protected void initialiseCvWriter()

initialiseCvWriter.

Specified by:

initialiseCvWriter in class AbstractXmlParticipantEvidenceWriter

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.

writeStoichiometry

protected void writeStoichiometry(ParticipantEvidence object)

writeStoichiometry.

Specified by:

writeStoichiometry in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a ParticipantEvidence object.

writeOtherAttributes

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

writeOtherAttributes.

Specified by:

writeOtherAttributes in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

writeAttributeList - a boolean.

Throws:

XMLStreamException - if any.

initialiseBiologicalRoleWriter

protected void initialiseBiologicalRoleWriter()

initialiseBiologicalRoleWriter.

Specified by:

initialiseBiologicalRoleWriter in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

initialiseInteractorWriter

protected void initialiseInteractorWriter()

initialiseInteractorWriter.

Specified by:

initialiseInteractorWriter in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

getParticipantCandidateWriter

public PsiXmlElementWriter<ExperimentalParticipantCandidate> getParticipantCandidateWriter()

Getter for the field participantCandidateWriter.

Returns:

a PsiXmlElementWriter object.

initialiseParticipantCandidateWriter

protected abstract void initialiseParticipantCandidateWriter()

initialiseParticipantCandidateWriter.

setParticipantCandidateWriter

public void setParticipantCandidateWriter(PsiXmlElementWriter<ExperimentalParticipantCandidate> 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<ParticipantEvidence,FeatureEvidence>

Parameters:

pool - a ParticipantPool object.

Throws:

XMLStreamException - if any.