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

Class XmlBinaryInteractionEvidenceWriter

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<BinaryInteractionEvidence>

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

All Implemented Interfaces:

CompactPsiXmlElementWriter<BinaryInteractionEvidence>, PsiXmlElementWriter<BinaryInteractionEvidence>, PsiXmlExtendedInteractionWriter<BinaryInteractionEvidence>, PsiXmlInteractionWriter<BinaryInteractionEvidence>

public class XmlBinaryInteractionEvidenceWriter
extends AbstractXmlInteractionEvidenceWriter<BinaryInteractionEvidence>
implements CompactPsiXmlElementWriter<BinaryInteractionEvidence>

Compact XML 3.0 writer for an expanded binary 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
XmlBinaryInteractionEvidenceWriter(XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for XmlBinaryInteractionEvidenceWriter.

Method Summary

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

XmlBinaryInteractionEvidenceWriter

public XmlBinaryInteractionEvidenceWriter(XMLStreamWriter writer,
                                          PsiXmlObjectCache objectIndex)

Constructor for XmlBinaryInteractionEvidenceWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

initialiseParticipantWriter

protected void initialiseParticipantWriter()

initialiseParticipantWriter.

Specified by:

initialiseParticipantWriter in class AbstractXmlInteractionWriter<BinaryInteractionEvidence,ParticipantEvidence>

writeAvailability

protected void writeAvailability(BinaryInteractionEvidence object)
                          throws XMLStreamException

writeAvailability.

Specified by:

writeAvailability in class AbstractXmlInteractionWriter<BinaryInteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeExperiments

protected CvTerm writeExperiments(BinaryInteractionEvidence object)
                           throws XMLStreamException

writeExperiments.

Overrides:

writeExperiments in class AbstractXmlInteractionEvidenceWriter<BinaryInteractionEvidence>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeAttributes

protected void writeAttributes(BinaryInteractionEvidence object)
                        throws XMLStreamException

writeAttributes.

Overrides:

writeAttributes in class AbstractXmlInteractionWriter<BinaryInteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.