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

Class AbstractXmlInteractionWriter<T extends Interaction>

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlInteractionWriter<T,Participant>

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25.AbstractXmlInteractionWriter<T>

All Implemented Interfaces:

PsiXmlElementWriter<T>, PsiXmlInteractionWriter<T>

Direct Known Subclasses:

AbstractXmlInteractionWriter, XmlBasicBinaryInteractionWriter, XmlBasicBinaryInteractionWriter, XmlBasicInteractionWriter, XmlBasicInteractionWriter

public abstract class AbstractXmlInteractionWriter<T extends Interaction>
extends AbstractXmlInteractionWriter<T,Participant>

Abstract writer of interaction in PSI-XML 2.5

Since:

12/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseInferredInteractionWriter()	initialiseInferredInteractionWriter.
protected void	initialiseInteractionTypeWriter()	initialiseInteractionTypeWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
protected void	writeAvailability(T object)	writeAvailability.
protected void	writeConfidences(T object)	writeConfidences.
protected void	writeInferredInteractions(T object)	writeInferredInteractions.
protected void	writeIntraMolecular(T object)	writeIntraMolecular.
protected void	writeModelled(T object)	writeModelled.
protected void	writeNegative(T object)	writeNegative.
protected void	writeOtherAttributes(T object)	writeOtherAttributes.
protected void	writeOtherProperties(T object)	writeOtherProperties.
protected void	writeParameters(T object)	writeParameters.
protected void	writeStartInteraction()	writeStartInteraction.

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

collectInferredInteractionsFrom, extractDefaultExperimentFrom, getAttributeWriter, getChecksumWriter, getDefaultExperiment, getExperimentWriter, getInferredInteractionWriter, getInteractionTypeWriter, getObjectIndex, getParticipantWriter, getStreamWriter, getVersion, getXrefWriter, initialiseDefaultExperiment, initialiseParticipantWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setDefaultExperiment, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeAttributes, writeComplexAsInteractor, writeExperimentDescription, writeExperimentRef, writeExperiments, writeInteractionType, writeNames, writeParticipants, writeXref, writeXrefFromInteractionIdentifiers, writeXrefFromInteractionXrefs

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractXmlInteractionWriter

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

Constructor for AbstractXmlInteractionWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Specified by:

initialiseXrefWriter in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Specified by:

initialiseExperimentWriter in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

initialiseInferredInteractionWriter

protected void initialiseInferredInteractionWriter()

initialiseInferredInteractionWriter.

Specified by:

initialiseInferredInteractionWriter in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

initialiseInteractionTypeWriter

protected void initialiseInteractionTypeWriter()

initialiseInteractionTypeWriter.

Specified by:

initialiseInteractionTypeWriter in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

writeInferredInteractions

protected void writeInferredInteractions(T object)
                                  throws XMLStreamException

writeInferredInteractions.

Specified by:

writeInferredInteractions in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeAvailability

protected void writeAvailability(T object)

writeAvailability.

Specified by:

writeAvailability in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

writeOtherAttributes

protected void writeOtherAttributes(T object)

writeOtherAttributes.

Specified by:

writeOtherAttributes in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

writeIntraMolecular

protected void writeIntraMolecular(T object)
                            throws XMLStreamException

writeIntraMolecular.

Overrides:

writeIntraMolecular in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeModelled

protected void writeModelled(T object)

writeModelled.

Specified by:

writeModelled in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

writeParameters

protected void writeParameters(T object)

writeParameters.

Specified by:

writeParameters in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

writeConfidences

protected void writeConfidences(T object)

writeConfidences.

Specified by:

writeConfidences in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

writeNegative

protected void writeNegative(T object)

writeNegative.

Specified by:

writeNegative in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

writeOtherProperties

protected void writeOtherProperties(T object)

writeOtherProperties.

Specified by:

writeOtherProperties in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Parameters:

object - a T object.

writeStartInteraction

protected void writeStartInteraction()
                              throws XMLStreamException

writeStartInteraction.

Specified by:

writeStartInteraction in class AbstractXmlInteractionWriter<T extends Interaction,Participant>

Throws:

XMLStreamException - if any.