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

Class XmlModelledBinaryInteractionWriter

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<ModelledBinaryInteraction>

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml25.XmlModelledBinaryInteractionWriter

All Implemented Interfaces:

CompactPsiXmlElementWriter<ModelledBinaryInteraction>, PsiXmlElementWriter<ModelledBinaryInteraction>, PsiXmlExtendedInteractionWriter<ModelledBinaryInteraction>, PsiXmlInteractionWriter<ModelledBinaryInteraction>

public class XmlModelledBinaryInteractionWriter
extends AbstractXmlModelledInteractionWriter<ModelledBinaryInteraction>
implements CompactPsiXmlElementWriter<ModelledBinaryInteraction>

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

Since:

15/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	initialiseParticipantWriter()	initialiseParticipantWriter.
protected void	writeAttributes(ModelledBinaryInteraction object)	writeAttributes.
protected CvTerm	writeExperiments(ModelledBinaryInteraction 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, 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

XmlModelledBinaryInteractionWriter

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

Constructor for XmlModelledBinaryInteractionWriter.

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<ModelledBinaryInteraction,ModelledParticipant>

writeExperiments

protected CvTerm writeExperiments(ModelledBinaryInteraction object)
                           throws XMLStreamException

writeExperiments.

Overrides:

writeExperiments in class AbstractXmlModelledInteractionWriter<ModelledBinaryInteraction>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeAttributes

protected void writeAttributes(ModelledBinaryInteraction object)
                        throws XMLStreamException

writeAttributes.

Overrides:

writeAttributes in class AbstractXmlModelledInteractionWriter<ModelledBinaryInteraction>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.