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

Class XmlInteractionEvidenceWriter

java.lang.Object

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

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

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

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30.AbstractXmlInteractionEvidenceWriter<InteractionEvidence>

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

All Implemented Interfaces:

CompactPsiXmlElementWriter<InteractionEvidence>, PsiXmlElementWriter<InteractionEvidence>, PsiXmlExtendedInteractionWriter<InteractionEvidence>, PsiXmlInteractionWriter<InteractionEvidence>

public class XmlInteractionEvidenceWriter
extends AbstractXmlInteractionEvidenceWriter<InteractionEvidence>
implements CompactPsiXmlElementWriter<InteractionEvidence>

Compact XML 3.0 writer for an expanded interaction evidence (having modelled, intramolecular properties, list of experiments, list of interaction types, etc.).

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

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

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

getCausalRelationshipWriter, getVariableParameterValueSetWriter, initialiseCausalRelationshipWriter, initialiseExperimentWriter, initialiseParameterWriter, setCausalRelationshipWriter, setVariableParameterValueSetWriter, writeCausalRelationships, writeExperimentalVariableValues, writeOtherProperties

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

extractDefaultExperimentsFrom, getAliasWriter, getDefaultExperiments, getXmlInferredInteractionWriter, initialiseConfidenceWriter, initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseXrefWriter, setAliasWriter, setDefaultExperiments, setXmlInferredInteractionWriter, writeExperimentDescription, writeExperimentRef, writeInferredInteractions, writeInteractionType, writeIntraMolecular, writeModelled, writeNames

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

extractDefaultExperimentFrom, getAvailabilityWriter, getConfidenceWriter, getParameterWriter, initialiseAvaliabilityWriter, initialiseDefaultExperiment, setAvailabilityWriter, setConfidenceWriter, setDefaultExperiment, setParameterWriter, writeAvailabilityDescription, writeAvailabilityRef, writeConfidences, writeNegative, writeOtherAttributes, writeParameters, writeStartInteraction

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, writeAttributes, 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.PsiXmlInteractionWriter

extractDefaultExperimentFrom, getDefaultExperiment, setComplexAsInteractor, setDefaultExperiment, writeComplexAsInteractor

Constructor Detail

XmlInteractionEvidenceWriter

public XmlInteractionEvidenceWriter(XMLStreamWriter writer,
                                    PsiXmlObjectCache objectIndex)

Constructor for XmlInteractionEvidenceWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

initialiseParticipantWriter

protected void initialiseParticipantWriter()

initialiseParticipantWriter.

Specified by:

initialiseParticipantWriter in class AbstractXmlInteractionWriter<InteractionEvidence,ParticipantEvidence>

writeAvailability

protected void writeAvailability(InteractionEvidence object)
                          throws XMLStreamException

writeAvailability.

Specified by:

writeAvailability in class AbstractXmlInteractionWriter<InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeExperiments

protected CvTerm writeExperiments(InteractionEvidence object)
                           throws XMLStreamException

writeExperiments.

Overrides:

writeExperiments in class AbstractXmlInteractionEvidenceWriter<InteractionEvidence>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.