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

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.xml30.AbstractXmlModelledInteractionWriter<ModelledBinaryInteraction>

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

All Implemented Interfaces:

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

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

Compact XML 3.0 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(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 void	writeOtherProperties(ModelledBinaryInteraction object)	writeOtherProperties.

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

extractDefaultExperimentsFrom, getAllosteryWriter, getBindingFeaturesWriter, getCausalRelationshipWriter, getDefaultExperiments, getOrganismWriter, getPreAssemblyWriter, initialiseCausalRelationshipWriter, initialiseConfidenceWriter, initialiseExperimentWriter, initialiseParameterWriter, setAllosteryWriter, setBindingFeaturesWriter, setCausalRelationshipWriter, setDefaultExperiments, setOrganismWriter, setPreAssemblyWriter, writeCausalRelationships, writeCooperativeEffect, writeCooperativeEffects, writeEvidenceType, writeExperimentDescription, writeExperimentRef, writeExperiments, writeInferredInteractions, writeInteractorType, writeIntraMolecular, writeOrganism, writeStartInteraction

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

initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseXrefWriter

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

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

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, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeComplexAsInteractor, writeInteractionType, 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.PsiXmlInteractionWriter

extractDefaultExperimentFrom, getDefaultExperiment, setComplexAsInteractor, setDefaultExperiment, writeComplexAsInteractor

Constructor Detail

XmlModelledBinaryInteractionWriter

public XmlModelledBinaryInteractionWriter(XMLStreamWriter writer,
                                          PsiXmlObjectCache objectIndex)

Constructor for XmlModelledBinaryInteractionWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

initialiseParticipantWriter

protected void initialiseParticipantWriter()

initialiseParticipantWriter.

Specified by:

initialiseParticipantWriter in class AbstractXmlInteractionWriter<ModelledBinaryInteraction,ModelledParticipant>

writeOtherProperties

protected void writeOtherProperties(ModelledBinaryInteraction object)
                             throws XMLStreamException

writeOtherProperties.

Overrides:

writeOtherProperties in class AbstractXmlModelledInteractionWriter<ModelledBinaryInteraction>

Parameters:

object - a T 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.