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

Class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

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.abstracts.xml30.AbstractXmlInteractionEvidenceWriter<I>

All Implemented Interfaces:

PsiXmlElementWriter<I>, PsiXmlInteractionWriter<I>

Direct Known Subclasses:

XmlBinaryInteractionEvidenceWriter, XmlBinaryInteractionEvidenceWriter, XmlInteractionEvidenceWriter, XmlInteractionEvidenceWriter

public abstract class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>
extends AbstractXmlInteractionEvidenceWriter<I>

Abstract class for interaction evidence writers in PSI-MI XML 3.0

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
PsiXmlCausalRelationshipWriter	getCausalRelationshipWriter()	Getter for the field causalRelationshipWriter.
PsiXmlElementWriter<VariableParameterValueSet>	getVariableParameterValueSetWriter()	Getter for the field variableParameterValueSetWriter.
protected void	initialiseCausalRelationshipWriter()	initialiseCausalRelationshipWriter.
protected void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseInferredInteractionWriter()	initialiseInferredInteractionWriter.
protected void	initialiseInteractionTypeWriter()	initialiseInteractionTypeWriter.
protected void	initialiseParameterWriter()	initialiseParameterWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
void	setCausalRelationshipWriter(PsiXmlCausalRelationshipWriter causalRelationshipWriter)	Setter for the field causalRelationshipWriter.
void	setVariableParameterValueSetWriter(PsiXmlElementWriter<VariableParameterValueSet> variableParameterValueSetWriter)	Setter for the field variableParameterValueSetWriter.
protected void	writeCausalRelationships(I object)	writeCausalRelationships.
protected void	writeExperimentalVariableValues(I object)	writeExperimentalVariableValues.
protected void	writeOtherProperties(I object)	writeOtherProperties.

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, writeExperiments, writeInferredInteractions, writeModelled, 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, initialiseParticipantWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeAttributes, writeAvailability, writeComplexAsInteractor, writeExperimentDescription, writeExperimentRef, writeInteractionType, writeIntraMolecular, writeNames, writeParticipants, writeXref, writeXrefFromInteractionIdentifiers, writeXrefFromInteractionXrefs

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractXmlInteractionEvidenceWriter

public AbstractXmlInteractionEvidenceWriter(XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlInteractionEvidenceWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getVariableParameterValueSetWriter

public PsiXmlElementWriter<VariableParameterValueSet> getVariableParameterValueSetWriter()

Getter for the field variableParameterValueSetWriter.

Returns:

a PsiXmlElementWriter object.

setVariableParameterValueSetWriter

public void setVariableParameterValueSetWriter(PsiXmlElementWriter<VariableParameterValueSet> variableParameterValueSetWriter)

Setter for the field variableParameterValueSetWriter.

Parameters:

variableParameterValueSetWriter - a PsiXmlElementWriter object.

getCausalRelationshipWriter

public PsiXmlCausalRelationshipWriter getCausalRelationshipWriter()

Getter for the field causalRelationshipWriter.

Returns:

a PsiXmlCausalRelationshipWriter object.

initialiseCausalRelationshipWriter

protected void initialiseCausalRelationshipWriter()

initialiseCausalRelationshipWriter.

setCausalRelationshipWriter

public void setCausalRelationshipWriter(PsiXmlCausalRelationshipWriter causalRelationshipWriter)

Setter for the field causalRelationshipWriter.

Parameters:

causalRelationshipWriter - a PsiXmlCausalRelationshipWriter object.

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Specified by:

initialiseXrefWriter in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Specified by:

initialiseExperimentWriter in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

initialiseConfidenceWriter

protected void initialiseConfidenceWriter()

initialiseConfidenceWriter.

Specified by:

initialiseConfidenceWriter in class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

initialiseParameterWriter

protected void initialiseParameterWriter()

initialiseParameterWriter.

Specified by:

initialiseParameterWriter in class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

initialiseInferredInteractionWriter

protected void initialiseInferredInteractionWriter()

initialiseInferredInteractionWriter.

Specified by:

initialiseInferredInteractionWriter in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

initialiseInteractionTypeWriter

protected void initialiseInteractionTypeWriter()

initialiseInteractionTypeWriter.

Specified by:

initialiseInteractionTypeWriter in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

writeOtherProperties

protected void writeOtherProperties(I object)
                             throws XMLStreamException

writeOtherProperties.

Specified by:

writeOtherProperties in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeCausalRelationships

protected void writeCausalRelationships(I object)
                                 throws XMLStreamException

writeCausalRelationships.

Parameters:

object - a I object.

Throws:

XMLStreamException - if any.

writeExperimentalVariableValues

protected void writeExperimentalVariableValues(I object)
                                        throws XMLStreamException

writeExperimentalVariableValues.

Parameters:

object - a I object.

Throws:

XMLStreamException - if any.