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

Class AbstractXmlExperimentWriter

java.lang.Object

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

All Implemented Interfaces:

PsiXmlElementWriter<Experiment>, PsiXmlExperimentWriter

Direct Known Subclasses:

XmlExperimentWriter, XmlExperimentWriter

public abstract class AbstractXmlExperimentWriter
extends Object
implements PsiXmlExperimentWriter

Abstract PSI-XML experiment writer

Since:

12/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
CvTerm	extractDefaultParticipantIdentificationMethod(Experiment exp)	extractDefaultParticipantIdentificationMethod.
PsiXmlElementWriter<Annotation>	getAttributeWriter()	Getter for the field attributeWriter.
PsiXmlElementWriter<Confidence>	getConfidenceWriter()	Getter for the field confidenceWriter.
Publication	getDefaultPublication()	getDefaultPublication.
PsiXmlVariableNameWriter<CvTerm>	getDetectionMethodWriter()	Getter for the field detectionMethodWriter.
PsiXmlElementWriter<Organism>	getHostOrganismWriter()	Getter for the field hostOrganismWriter.
protected PsiXmlObjectCache	getObjectIndex()	Getter for the field objectIndex.
PsiXmlPublicationWriter	getPublicationWriter()	Getter for the field publicationWriter.
protected XMLStreamWriter	getStreamWriter()	Getter for the field streamWriter.
protected PsiXmlVersion	getVersion()
PsiXmlXrefWriter	getXrefWriter()	Getter for the field xrefWriter.
protected abstract void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseDefaultPublication()	initialiseDefaultPublication.
protected abstract void	initialiseDetectionMethodWriter()	initialiseDetectionMethodWriter.
protected abstract void	initialiseHostOrganismWriter()	initialiseHostOrganismWriter.
protected abstract void	initialisePublicationWriter()	initialisePublicationWriter.
protected abstract void	initialiseXrefWriter()	initialiseXrefWriter.
void	setAttributeWriter(PsiXmlElementWriter<Annotation> attributeWriter)	Setter for the field attributeWriter.
void	setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)	Setter for the field confidenceWriter.
void	setDefaultPublication(Publication pub)	Sets the default publication to write in case an experiment does not have a publication
void	setDetectionMethodWriter(PsiXmlVariableNameWriter<CvTerm> detectionMethodWriter)	Setter for the field detectionMethodWriter.
void	setHostOrganismWriter(PsiXmlElementWriter<Organism> hostOrganismWriter)	Setter for the field hostOrganismWriter.
void	setPublicationWriter(PsiXmlPublicationWriter publicationWriter)	Setter for the field publicationWriter.
void	setXrefWriter(PsiXmlXrefWriter xrefWriter)	Setter for the field xrefWriter.
void	write(Experiment object)	write.
protected void	writeAttributes(Experiment object)	writeAttributes.
protected void	writeConfidences(Experiment object)	writeConfidences.
CvTerm	writeExperiment(Experiment object)	writeExperiment.
protected abstract void	writeExperimentXrefs(Experiment object, String imexId)	writeExperimentXrefs.
protected void	writeHostOrganism(Experiment object)	writeHostOrganism.
protected void	writeInteractiondetectionMethod(Experiment object)	writeInteractiondetectionMethod.
protected void	writeNames(Experiment object)	writeNames.
protected abstract void	writeOtherAttributes(Experiment object, boolean needToWriteAttributeList)	writeOtherAttributes.
protected void	writeOtherProperties(Experiment object)	writeOtherProperties.
protected CvTerm	writeParticipantIdentificationMethod(Experiment object)	writeParticipantIdentificationMethod.
protected void	writePublicationAndXrefs(Experiment object)	writePublicationAndXrefs.
protected abstract void	writeVariableParameters(Experiment object)	writeVariableParameters.
protected void	writeXrefFromExperimentXrefs(Experiment object, String imexId)	writeXrefFromExperimentXrefs.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractXmlExperimentWriter

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

Constructor for AbstractXmlExperimentWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getPublicationWriter

public PsiXmlPublicationWriter getPublicationWriter()

Getter for the field publicationWriter.

Returns:

a PsiXmlPublicationWriter object.

initialisePublicationWriter

protected abstract void initialisePublicationWriter()

initialisePublicationWriter.

setPublicationWriter

public void setPublicationWriter(PsiXmlPublicationWriter publicationWriter)

Setter for the field publicationWriter.

Parameters:

publicationWriter - a PsiXmlPublicationWriter 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.

getHostOrganismWriter

public PsiXmlElementWriter<Organism> getHostOrganismWriter()

Getter for the field hostOrganismWriter.

Returns:

a PsiXmlElementWriter object.

initialiseHostOrganismWriter

protected abstract void initialiseHostOrganismWriter()

initialiseHostOrganismWriter.

setHostOrganismWriter

public void setHostOrganismWriter(PsiXmlElementWriter<Organism> hostOrganismWriter)

Setter for the field hostOrganismWriter.

Parameters:

hostOrganismWriter - a PsiXmlElementWriter object.

getDetectionMethodWriter

public PsiXmlVariableNameWriter<CvTerm> getDetectionMethodWriter()

Getter for the field detectionMethodWriter.

Returns:

a PsiXmlVariableNameWriter object.

initialiseDetectionMethodWriter

protected abstract void initialiseDetectionMethodWriter()

initialiseDetectionMethodWriter.

setDetectionMethodWriter

public void setDetectionMethodWriter(PsiXmlVariableNameWriter<CvTerm> detectionMethodWriter)

Setter for the field detectionMethodWriter.

Parameters:

detectionMethodWriter - 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.

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.

writeExperiment

public CvTerm writeExperiment(Experiment object)
                       throws MIIOException

writeExperiment.

Specified by:

writeExperiment in interface PsiXmlExperimentWriter

Parameters:

object - the experiment to write

Returns:

the participant identification method used by the writer when writing the experiment. Can be null if no participant identification method has been written.

Throws:

MIIOException - if any.

write

public void write(Experiment object)
           throws MIIOException

write.

Specified by:

write in interface PsiXmlElementWriter<Experiment>

Parameters:

object - a T object.

Throws:

MIIOException - if any.

extractDefaultParticipantIdentificationMethod

public CvTerm extractDefaultParticipantIdentificationMethod(Experiment exp)

extractDefaultParticipantIdentificationMethod.

Specified by:

extractDefaultParticipantIdentificationMethod in interface PsiXmlExperimentWriter

Parameters:

exp - a Experiment object.

Returns:

the default participant identification method associated with this experiment

writeParticipantIdentificationMethod

protected CvTerm writeParticipantIdentificationMethod(Experiment object)

writeParticipantIdentificationMethod.

Parameters:

object - a Experiment object.

Returns:

a CvTerm object.

writeVariableParameters

protected abstract void writeVariableParameters(Experiment object)
                                         throws XMLStreamException

writeVariableParameters.

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeOtherProperties

protected void writeOtherProperties(Experiment object)
                             throws XMLStreamException

writeOtherProperties.

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeConfidences

protected void writeConfidences(Experiment object)
                         throws XMLStreamException

writeConfidences.

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeAttributes

protected void writeAttributes(Experiment object)
                        throws XMLStreamException

writeAttributes.

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeOtherAttributes

protected abstract void writeOtherAttributes(Experiment object,
                                             boolean needToWriteAttributeList)
                                      throws XMLStreamException

writeOtherAttributes.

Parameters:

object - a Experiment object.

needToWriteAttributeList - a boolean.

Throws:

XMLStreamException - if any.

writeInteractiondetectionMethod

protected void writeInteractiondetectionMethod(Experiment object)
                                        throws XMLStreamException

writeInteractiondetectionMethod.

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeHostOrganism

protected void writeHostOrganism(Experiment object)
                          throws XMLStreamException

writeHostOrganism.

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writePublicationAndXrefs

protected void writePublicationAndXrefs(Experiment object)
                                 throws XMLStreamException

writePublicationAndXrefs.

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeExperimentXrefs

protected abstract void writeExperimentXrefs(Experiment object,
                                             String imexId)
                                      throws XMLStreamException

writeExperimentXrefs.

Parameters:

object - a Experiment object.

imexId - a String object.

Throws:

XMLStreamException - if any.

writeXrefFromExperimentXrefs

protected void writeXrefFromExperimentXrefs(Experiment object,
                                            String imexId)
                                     throws XMLStreamException

writeXrefFromExperimentXrefs.

Parameters:

object - a Experiment object.

imexId - a String object.

Throws:

XMLStreamException - if any.

writeNames

protected void writeNames(Experiment object)
                   throws XMLStreamException

writeNames.

Parameters:

object - a Experiment 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.

getDefaultPublication

public Publication getDefaultPublication()

getDefaultPublication.

Specified by:

getDefaultPublication in interface PsiXmlExperimentWriter

Returns:

the default publication. It cannot be null

setDefaultPublication

public void setDefaultPublication(Publication pub)

Sets the default publication to write in case an experiment does not have a publication

Specified by:

setDefaultPublication in interface PsiXmlExperimentWriter

Parameters:

pub - a Publication object.

initialiseDefaultPublication

protected void initialiseDefaultPublication()

initialiseDefaultPublication.

getVersion

protected PsiXmlVersion getVersion()