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

Class XmlNamedModelledInteractionWriter

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.abstracts.xml30.AbstractXmlModelledInteractionWriter<ModelledInteraction>

psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30.XmlModelledInteractionWriter

psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30.XmlNamedModelledInteractionWriter

All Implemented Interfaces:

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

public class XmlNamedModelledInteractionWriter
extends XmlModelledInteractionWriter

Expanded XML 3.0 writer for a modelled interaction (ignore experimental details) which have a fullname and aliases in addition to the shortname. It will write cooperative effects as attributes

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
XmlNamedModelledInteractionWriter(XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for XmlNamedModelledInteractionWriter.

Method Summary

Modifier and Type	Method	Description
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseParticipantWriter()	initialiseParticipantWriter.

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30.XmlModelledInteractionWriter

writeExperiments

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

getAllosteryWriter, getBindingFeaturesWriter, getCausalRelationshipWriter, getOrganismWriter, getPreAssemblyWriter, initialiseCausalRelationshipWriter, initialiseConfidenceWriter, initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseParameterWriter, initialiseXrefWriter, setAllosteryWriter, setBindingFeaturesWriter, setCausalRelationshipWriter, setOrganismWriter, setPreAssemblyWriter, writeCausalRelationships, writeCooperativeEffect, writeCooperativeEffects, writeEvidenceType, writeExperimentDescription, writeExperimentRef, writeInferredInteractions, writeInteractorType, writeOrganism, writeOtherProperties, writeStartInteraction

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

getAliasWriter, getConfidenceWriter, getParameterWriter, initialiseDefaultExperiment, setAliasWriter, setConfidenceWriter, setDefaultExperiment, 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, 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, writeIntraMolecular, 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

Constructor Detail

XmlNamedModelledInteractionWriter

public XmlNamedModelledInteractionWriter(XMLStreamWriter writer,
                                         PsiXmlObjectCache objectIndex)

Constructor for XmlNamedModelledInteractionWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Overrides:

initialiseExperimentWriter in class AbstractXmlModelledInteractionWriter<ModelledInteraction>

initialiseParticipantWriter

protected void initialiseParticipantWriter()

initialiseParticipantWriter.

Overrides:

initialiseParticipantWriter in class XmlModelledInteractionWriter