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

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

All Implemented Interfaces:

PsiXmlElementWriter<ParticipantEvidence>, PsiXmlParticipantWriter<ParticipantEvidence>

Direct Known Subclasses:

AbstractXmlParticipantEvidenceWriter, AbstractXmlParticipantEvidenceWriter

public abstract class AbstractXmlParticipantEvidenceWriter
extends AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Abstract class for writer of participant evidences

Since:

14/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
PsiXmlElementWriter<Confidence>	getConfidenceWriter()	Getter for the field confidenceWriter.
PsiXmlVariableNameWriter<CvTerm>	getExperimentalCvWriter()	getExperimentalCvWriter.
PsiXmlElementWriter<Organism>	getHostOrganismWriter()	Getter for the field hostOrganismWriter.
PsiXmlElementWriter<Parameter>	getParameterWriter()	Getter for the field parameterWriter.
protected abstract void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected abstract void	initialiseCvWriter()	initialiseCvWriter.
protected abstract void	initialiseHostOrganismWriter()	initialiseHostOrganismWriter.
protected abstract void	initialiseParameterWriter()	initialiseParameterWriter.
void	setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)	Setter for the field confidenceWriter.
void	setExperimentalCvWriter(PsiXmlVariableNameWriter<CvTerm> cvWriter)	setExperimentalCvWriter.
void	setHostOrganismWriter(PsiXmlElementWriter<Organism> hostOrganismWriter)	Setter for the field hostOrganismWriter.
void	setParameterWriter(PsiXmlElementWriter<Parameter> parameterWriter)	Setter for the field parameterWriter.
protected void	writeConfidences(ParticipantEvidence object)	writeConfidences.
protected void	writeExperimentalInteractor(ParticipantEvidence object)	writeExperimentalInteractor.
protected void	writeExperimentalPreparations(ParticipantEvidence object)	writeExperimentalPreparations.
protected void	writeExperimentalRoles(ParticipantEvidence object)	writeExperimentalRoles.
protected void	writeHostOrganisms(ParticipantEvidence object)	writeHostOrganisms.
protected void	writeParameters(ParticipantEvidence object)	writeParameters.
protected void	writeParticipantIdentificationMethods(ParticipantEvidence object, CvTerm experimentMethod)	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, initialiseBiologicalRoleWriter, initialiseFeatureWriter, initialiseInteractorWriter, initialiseXrefWriter, setAliasWriter, setAttributeWriter, setBiologicalRoleWriter, setComplexAsInteractor, setFeatureWriter, setInteractorWriter, setXrefWriter, write, writeAttributes, writeBiologicalRole, writeComplexAsInteractor, writeFeatures, writeInteractor, writeMolecule, writeMoleculeDescription, writeMoleculeRef, writeNames, writeOtherAttributes, writeParticipant, writeParticipantPool, writeStoichiometry, 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(PsiXmlVersion version,
                                            XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlParticipantEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getExperimentalCvWriter

public PsiXmlVariableNameWriter<CvTerm> getExperimentalCvWriter()

getExperimentalCvWriter.

Returns:

a PsiXmlVariableNameWriter object.

initialiseCvWriter

protected abstract void initialiseCvWriter()

initialiseCvWriter.

setExperimentalCvWriter

public void setExperimentalCvWriter(PsiXmlVariableNameWriter<CvTerm> cvWriter)

setExperimentalCvWriter.

Parameters:

cvWriter - a PsiXmlVariableNameWriter object.

getConfidenceWriter

public PsiXmlElementWriter<Confidence> getConfidenceWriter()

Getter for the field confidenceWriter.

Returns:

a PsiXmlElementWriter object.

initialiseConfidenceWriter

protected abstract void initialiseConfidenceWriter()

initialiseConfidenceWriter.

setConfidenceWriter

public void setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)

Setter for the field confidenceWriter.

Parameters:

confidenceWriter - a PsiXmlElementWriter object.

setHostOrganismWriter

public void setHostOrganismWriter(PsiXmlElementWriter<Organism> hostOrganismWriter)

Setter for the field hostOrganismWriter.

Parameters:

hostOrganismWriter - a PsiXmlElementWriter object.

getHostOrganismWriter

public PsiXmlElementWriter<Organism> getHostOrganismWriter()

Getter for the field hostOrganismWriter.

Returns:

a PsiXmlElementWriter object.

initialiseHostOrganismWriter

protected abstract void initialiseHostOrganismWriter()

initialiseHostOrganismWriter.

getParameterWriter

public PsiXmlElementWriter<Parameter> getParameterWriter()

Getter for the field parameterWriter.

Returns:

a PsiXmlElementWriter object.

initialiseParameterWriter

protected abstract void initialiseParameterWriter()

initialiseParameterWriter.

setParameterWriter

public void setParameterWriter(PsiXmlElementWriter<Parameter> parameterWriter)

Setter for the field parameterWriter.

Parameters:

parameterWriter - a PsiXmlElementWriter object.

writeExperimentalPreparations

protected void writeExperimentalPreparations(ParticipantEvidence object)
                                      throws XMLStreamException

writeExperimentalPreparations.

Specified by:

writeExperimentalPreparations in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeExperimentalRoles

protected void writeExperimentalRoles(ParticipantEvidence object)
                               throws XMLStreamException

writeExperimentalRoles.

Specified by:

writeExperimentalRoles in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeParticipantIdentificationMethods

protected void writeParticipantIdentificationMethods(ParticipantEvidence object,
                                                     CvTerm experimentMethod)
                                              throws XMLStreamException

writeParticipantIdentificationMethods.

Specified by:

writeParticipantIdentificationMethods in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

experimentMethod - a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperimentalInteractor

protected void writeExperimentalInteractor(ParticipantEvidence object)
                                    throws XMLStreamException

writeExperimentalInteractor.

Specified by:

writeExperimentalInteractor in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeHostOrganisms

protected void writeHostOrganisms(ParticipantEvidence object)
                           throws XMLStreamException

writeHostOrganisms.

Specified by:

writeHostOrganisms in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeConfidences

protected void writeConfidences(ParticipantEvidence object)
                         throws XMLStreamException

writeConfidences.

Specified by:

writeConfidences in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.

writeParameters

protected void writeParameters(ParticipantEvidence object)
                        throws XMLStreamException

writeParameters.

Specified by:

writeParameters in class AbstractXmlParticipantWriter<ParticipantEvidence,FeatureEvidence>

Parameters:

object - a P object.

Throws:

XMLStreamException - if any.