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

Class XmlModelledInteractionWriter

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlInteractionWriter<I,ModelledParticipant>

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlModelledInteractionWriter<I>

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.AbstractXmlModelledInteractionWriter<I>

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.AbstractXmlModelledInteractionWriter<ModelledInteraction>

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml25.XmlModelledInteractionWriter

All Implemented Interfaces:

ExpandedPsiXmlElementWriter<ModelledInteraction>, PsiXmlElementWriter<ModelledInteraction>, PsiXmlExtendedInteractionWriter<ModelledInteraction>, PsiXmlInteractionWriter<ModelledInteraction>

public class XmlModelledInteractionWriter
extends AbstractXmlModelledInteractionWriter<ModelledInteraction>
implements ExpandedPsiXmlElementWriter<ModelledInteraction>

Expanded XML 2.5 writer for an expanded modelled interaction (ignore experimental details). It will write cooperative effects as attributes It will write intra-molecular property, names, interaction types and experiments

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	initialiseParticipantWriter()	initialiseParticipantWriter.
protected CvTerm	writeExperiments(ModelledInteraction object)	writeExperiments.

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.AbstractXmlModelledInteractionWriter

extractDefaultExperimentFrom, extractDefaultExperimentsFrom, getXmlInferredInteractionWriter, initialiseConfidenceWriter, initialiseDefaultExperiment, initialiseExperimentWriter, initialiseParameterWriter, setDefaultExperiment, setXmlInferredInteractionWriter, writeCooperativeEffect, writeCooperativeEffectAttribute, writeExperimentDescription, writeExperimentRef, writeInferredInteractions, writeInteractionType, writeOtherProperties, writeStartInteraction

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.AbstractXmlModelledInteractionWriter

getDefaultExperiments, initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseXrefWriter, setDefaultExperiments, writeIntraMolecular

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

getAliasWriter, getConfidenceWriter, getParameterWriter, setAliasWriter, setConfidenceWriter, setParameterWriter, writeAttributes, writeAvailability, writeConfidences, writeModelled, writeNames, writeNegative, writeOtherAttributes, writeParameters

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

collectInferredInteractionsFrom, getAttributeWriter, getChecksumWriter, getDefaultExperiment, getExperimentWriter, getInferredInteractionWriter, getInteractionTypeWriter, getObjectIndex, getParticipantWriter, getStreamWriter, getVersion, getXrefWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeComplexAsInteractor, writeParticipants, writeXref, writeXrefFromInteractionIdentifiers, writeXrefFromInteractionXrefs

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.xml.io.writer.elements.PsiXmlElementWriter

write

Methods inherited from interface psidev.psi.mi.jami.xml.io.writer.elements.PsiXmlExtendedInteractionWriter

getDefaultExperiments, setDefaultExperiments

Methods inherited from interface psidev.psi.mi.jami.xml.io.writer.elements.PsiXmlInteractionWriter

getDefaultExperiment, setComplexAsInteractor, writeComplexAsInteractor

Constructor Detail

XmlModelledInteractionWriter

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

Constructor for XmlModelledInteractionWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

initialiseParticipantWriter

protected void initialiseParticipantWriter()

initialiseParticipantWriter.

Specified by:

initialiseParticipantWriter in class AbstractXmlInteractionWriter<ModelledInteraction,ModelledParticipant>

writeExperiments

protected CvTerm writeExperiments(ModelledInteraction object)
                           throws XMLStreamException

writeExperiments.

Overrides:

writeExperiments in class AbstractXmlModelledInteractionWriter<ModelledInteraction>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.