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

Class XmlExperimentWriter

java.lang.Object

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

psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30.XmlExperimentWriter

psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30.XmlNamedExperimentWriter

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30.XmlExperimentWriter

All Implemented Interfaces:

PsiXmlElementWriter<Experiment>, PsiXmlExperimentWriter

public class XmlExperimentWriter
extends XmlNamedExperimentWriter

XML 3.0 writer for expanded experiments having participant identification method, feature detection method and a list of host organisms

Since:

13/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
CvTerm	extractDefaultParticipantIdentificationMethod(Experiment exp)	extractDefaultParticipantIdentificationMethod.
protected void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseDetectionMethodWriter()	initialiseDetectionMethodWriter.
protected void	initialiseHostOrganismWriter()	initialiseHostOrganismWriter.
protected void	initialisePublicationWriter()	initialisePublicationWriter.
protected void	initialiseVariableParameterWriter()	initialiseVariableParameterWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
protected void	writeHostOrganism(Experiment object)	writeHostOrganism.
protected void	writeOtherProperties(Experiment object)	writeOtherProperties.
protected CvTerm	writeParticipantIdentificationMethod(Experiment object)	writeParticipantIdentificationMethod.

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30.XmlNamedExperimentWriter

getAliasWriter, setAliasWriter, writeNames

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30.XmlExperimentWriter

getVariableParameterWriter, setVariableParameterWriter, writeExperimentXrefs, writeOtherAttributes, writeVariableParameters

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

getAttributeWriter, getConfidenceWriter, getDefaultPublication, getDetectionMethodWriter, getHostOrganismWriter, getObjectIndex, getPublicationWriter, getStreamWriter, getVersion, getXrefWriter, initialiseDefaultPublication, setAttributeWriter, setConfidenceWriter, setDefaultPublication, setDetectionMethodWriter, setHostOrganismWriter, setPublicationWriter, setXrefWriter, write, writeAttributes, writeConfidences, writeExperiment, writeInteractiondetectionMethod, writePublicationAndXrefs, writeXrefFromExperimentXrefs

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlExperimentWriter

public XmlExperimentWriter(XMLStreamWriter writer,
                           PsiXmlObjectCache objectIndex)

Constructor for XmlExperimentWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

writeParticipantIdentificationMethod

protected CvTerm writeParticipantIdentificationMethod(Experiment object)

writeParticipantIdentificationMethod.

Overrides:

writeParticipantIdentificationMethod in class AbstractXmlExperimentWriter

Parameters:

object - a Experiment object.

Returns:

a CvTerm object.

extractDefaultParticipantIdentificationMethod

public CvTerm extractDefaultParticipantIdentificationMethod(Experiment exp)

extractDefaultParticipantIdentificationMethod.

Specified by:

extractDefaultParticipantIdentificationMethod in interface PsiXmlExperimentWriter

Overrides:

extractDefaultParticipantIdentificationMethod in class AbstractXmlExperimentWriter

Parameters:

exp - a Experiment object.

Returns:

the default participant identification method associated with this experiment

writeOtherProperties

protected void writeOtherProperties(Experiment object)
                             throws XMLStreamException

writeOtherProperties.

Overrides:

writeOtherProperties in class AbstractXmlExperimentWriter

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeHostOrganism

protected void writeHostOrganism(Experiment object)
                          throws XMLStreamException

writeHostOrganism.

Overrides:

writeHostOrganism in class AbstractXmlExperimentWriter

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

initialisePublicationWriter

protected void initialisePublicationWriter()

initialisePublicationWriter.

Overrides:

initialisePublicationWriter in class XmlExperimentWriter

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Overrides:

initialiseXrefWriter in class XmlExperimentWriter

initialiseHostOrganismWriter

protected void initialiseHostOrganismWriter()

initialiseHostOrganismWriter.

Overrides:

initialiseHostOrganismWriter in class XmlExperimentWriter

initialiseConfidenceWriter

protected void initialiseConfidenceWriter()

initialiseConfidenceWriter.

Overrides:

initialiseConfidenceWriter in class XmlExperimentWriter

initialiseDetectionMethodWriter

protected void initialiseDetectionMethodWriter()

initialiseDetectionMethodWriter.

Overrides:

initialiseDetectionMethodWriter in class XmlExperimentWriter

initialiseVariableParameterWriter

protected void initialiseVariableParameterWriter()

initialiseVariableParameterWriter.

Overrides:

initialiseVariableParameterWriter in class XmlExperimentWriter