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

Class XmlComplexWriter

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<Complex>

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

All Implemented Interfaces:

CompactPsiXmlElementWriter<Complex>, PsiXmlElementWriter<Complex>, PsiXmlExtendedInteractionWriter<Complex>, PsiXmlInteractionWriter<Complex>

public class XmlComplexWriter
extends AbstractXmlModelledInteractionWriter<Complex>
implements CompactPsiXmlElementWriter<Complex>

Compact XML 2.5 writer for an expanded biological complex (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
XmlComplexWriter(PsiXmlVersion version, XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for XmlComplexWriter.

Method Summary

Modifier and Type	Method	Description
Experiment	extractDefaultExperimentFrom(Complex interaction)	extractDefaultExperimentFrom.
List<Experiment>	extractDefaultExperimentsFrom(Complex interaction)	extractDefaultExperimentsFrom.
protected void	initialiseParticipantWriter()	initialiseParticipantWriter.
protected CvTerm	writeExperiments(Complex object)	writeExperiments.

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

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

XmlComplexWriter

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

Constructor for XmlComplexWriter.

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<Complex,ModelledParticipant>

writeExperiments

protected CvTerm writeExperiments(Complex object)
                           throws XMLStreamException

writeExperiments.

Overrides:

writeExperiments in class AbstractXmlModelledInteractionWriter<Complex>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

extractDefaultExperimentFrom

public Experiment extractDefaultExperimentFrom(Complex interaction)

extractDefaultExperimentFrom.

Specified by:

extractDefaultExperimentFrom in interface PsiXmlInteractionWriter<Complex>

Overrides:

extractDefaultExperimentFrom in class AbstractXmlModelledInteractionWriter<Complex>

Parameters:

interaction - a T object.

Returns:

the default experiment for this interaction

extractDefaultExperimentsFrom

public List<Experiment> extractDefaultExperimentsFrom(Complex interaction)

extractDefaultExperimentsFrom.

Specified by:

extractDefaultExperimentsFrom in interface PsiXmlExtendedInteractionWriter<Complex>

Overrides:

extractDefaultExperimentsFrom in class AbstractXmlModelledInteractionWriter<Complex>

Parameters:

interaction - a T object.

Returns:

the default experiments for this interaction