Package psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25

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.xml25.XmlExperimentWriter

All Implemented Interfaces:

PsiXmlElementWriter<Experiment>, PsiXmlExperimentWriter

Direct Known Subclasses:

XmlNamedExperimentWriter

public class XmlExperimentWriter
extends AbstractXmlExperimentWriter

PSI-XML 2.5 experiment writer

Since:

12/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseDetectionMethodWriter()	initialiseDetectionMethodWriter.
protected void	initialiseHostOrganismWriter()	initialiseHostOrganismWriter.
protected void	initialisePublicationWriter()	initialisePublicationWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
protected void	writeExperimentXrefs(Experiment object, String imexId)	writeExperimentXrefs.
protected void	writeImexId(String nodeName, String imexId)	writeImexId.
protected void	writeOtherAttributes(Experiment object, boolean needToWriteAttributeList)	writeOtherAttributes.
protected void	writeVariableParameters(Experiment object)	writeVariableParameters.
protected void	writeXrefFromExperimentXrefs(Experiment object, String imexId)	writeXrefFromExperimentXrefs.

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlExperimentWriter

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

Constructor for XmlExperimentWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

writeVariableParameters

protected void writeVariableParameters(Experiment object)
                                throws XMLStreamException

writeVariableParameters.

Specified by:

writeVariableParameters in class AbstractXmlExperimentWriter

Parameters:

object - a Experiment object.

Throws:

XMLStreamException - if any.

writeOtherAttributes

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

writeOtherAttributes.

Specified by:

writeOtherAttributes in class AbstractXmlExperimentWriter

Parameters:

object - a Experiment object.

needToWriteAttributeList - a boolean.

Throws:

XMLStreamException - if any.

writeExperimentXrefs

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

writeExperimentXrefs.

Specified by:

writeExperimentXrefs in class AbstractXmlExperimentWriter

Parameters:

object - a Experiment object.

imexId - a String object.

Throws:

XMLStreamException - if any.

writeXrefFromExperimentXrefs

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

writeXrefFromExperimentXrefs.

Overrides:

writeXrefFromExperimentXrefs in class AbstractXmlExperimentWriter

Parameters:

object - a Experiment object.

imexId - a String object.

Throws:

XMLStreamException - if any.

writeImexId

protected void writeImexId(String nodeName,
                           String imexId)
                    throws XMLStreamException

writeImexId.

Parameters:

nodeName - a String object.

imexId - a String object.

Throws:

XMLStreamException - if any.

initialisePublicationWriter

protected void initialisePublicationWriter()

initialisePublicationWriter.

Specified by:

initialisePublicationWriter in class AbstractXmlExperimentWriter

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Specified by:

initialiseXrefWriter in class AbstractXmlExperimentWriter

initialiseHostOrganismWriter

protected void initialiseHostOrganismWriter()

initialiseHostOrganismWriter.

Specified by:

initialiseHostOrganismWriter in class AbstractXmlExperimentWriter

initialiseConfidenceWriter

protected void initialiseConfidenceWriter()

initialiseConfidenceWriter.

Specified by:

initialiseConfidenceWriter in class AbstractXmlExperimentWriter

initialiseDetectionMethodWriter

protected void initialiseDetectionMethodWriter()

initialiseDetectionMethodWriter.

Specified by:

initialiseDetectionMethodWriter in class AbstractXmlExperimentWriter