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

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>

All Implemented Interfaces:

PsiXmlElementWriter<I>, PsiXmlInteractionWriter<I>

Direct Known Subclasses:

AbstractXmlInteractionEvidenceWriter, AbstractXmlInteractionEvidenceWriter, AbstractXmlInteractionEvidenceWriter

public abstract class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>
extends AbstractXmlInteractionWriter<I,ParticipantEvidence>

Abstract class for interaction evidence writers

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
Experiment	extractDefaultExperimentFrom(I interaction)	extractDefaultExperimentFrom.
PsiXmlElementWriter<String>	getAvailabilityWriter()	Getter for the field availabilityWriter.
PsiXmlElementWriter<Confidence>	getConfidenceWriter()	Getter for the field confidenceWriter.
PsiXmlParameterWriter	getParameterWriter()	Getter for the field parameterWriter.
protected void	initialiseAvaliabilityWriter()	initialiseAvaliabilityWriter.
protected abstract void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseDefaultExperiment()	initialiseDefaultExperiment.
protected abstract void	initialiseParameterWriter()	initialiseParameterWriter.
void	setAvailabilityWriter(PsiXmlElementWriter<String> availabilityWriter)	Setter for the field availabilityWriter.
void	setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)	Setter for the field confidenceWriter.
void	setDefaultExperiment(Experiment defaultExperiment)	Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	setParameterWriter(PsiXmlParameterWriter parameterWriter)	Setter for the field parameterWriter.
protected void	writeAvailabilityDescription(String availability)	writeAvailabilityDescription.
protected void	writeAvailabilityRef(String availability)	writeAvailabilityRef.
protected void	writeConfidences(I object)	writeConfidences.
protected CvTerm	writeExperiments(I object)	writeExperiments.
protected void	writeInferredInteractions(I object)	writeInferredInteractions.
protected void	writeModelled(I object)	writeModelled.
protected void	writeNegative(I object)	writeNegative.
protected void	writeOtherAttributes(I object)	writeOtherAttributes.
protected void	writeParameters(I object)	writeParameters.
protected void	writeStartInteraction()	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, initialiseExperimentWriter, initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseParticipantWriter, initialiseXrefWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeAttributes, writeAvailability, writeComplexAsInteractor, writeExperimentDescription, writeExperimentRef, writeInteractionType, writeIntraMolecular, writeNames, writeOtherProperties, 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(PsiXmlVersion version,
                                            XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlInteractionEvidenceWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getAvailabilityWriter

public PsiXmlElementWriter<String> getAvailabilityWriter()

Getter for the field availabilityWriter.

Returns:

a PsiXmlElementWriter object.

initialiseAvaliabilityWriter

protected void initialiseAvaliabilityWriter()

initialiseAvaliabilityWriter.

setAvailabilityWriter

public void setAvailabilityWriter(PsiXmlElementWriter<String> availabilityWriter)

Setter for the field availabilityWriter.

Parameters:

availabilityWriter - a PsiXmlElementWriter object.

getConfidenceWriter

public PsiXmlElementWriter<Confidence> getConfidenceWriter()

Getter for the field confidenceWriter.

Returns:

a PsiXmlElementWriter object.

initialiseConfidenceWriter

protected abstract void initialiseConfidenceWriter()

initialiseConfidenceWriter.

setConfidenceWriter

public void setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)

Setter for the field confidenceWriter.

Parameters:

confidenceWriter - a PsiXmlElementWriter object.

getParameterWriter

public PsiXmlParameterWriter getParameterWriter()

Getter for the field parameterWriter.

Returns:

a PsiXmlParameterWriter object.

initialiseParameterWriter

protected abstract void initialiseParameterWriter()

initialiseParameterWriter.

setParameterWriter

public void setParameterWriter(PsiXmlParameterWriter parameterWriter)

Setter for the field parameterWriter.

Parameters:

parameterWriter - a PsiXmlParameterWriter object.

initialiseDefaultExperiment

protected void initialiseDefaultExperiment()

initialiseDefaultExperiment.

Overrides:

initialiseDefaultExperiment in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

setDefaultExperiment

public void setDefaultExperiment(Experiment defaultExperiment)

Sets the default experiment that will be used to write a valid XML file even if the interaction does not have any valid experiment

Specified by:

setDefaultExperiment in interface PsiXmlInteractionWriter<I extends InteractionEvidence>

Overrides:

setDefaultExperiment in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

defaultExperiment - : default experiment

extractDefaultExperimentFrom

public Experiment extractDefaultExperimentFrom(I interaction)

extractDefaultExperimentFrom.

Specified by:

extractDefaultExperimentFrom in interface PsiXmlInteractionWriter<I extends InteractionEvidence>

Overrides:

extractDefaultExperimentFrom in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

interaction - a T object.

Returns:

the default experiment for this interaction

writeExperiments

protected CvTerm writeExperiments(I object)
                           throws XMLStreamException

writeExperiments.

Specified by:

writeExperiments in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeOtherAttributes

protected void writeOtherAttributes(I object)
                             throws XMLStreamException

writeOtherAttributes.

Specified by:

writeOtherAttributes in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeModelled

protected void writeModelled(I object)
                      throws XMLStreamException

writeModelled.

Specified by:

writeModelled in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeParameters

protected void writeParameters(I object)
                        throws XMLStreamException

writeParameters.

Specified by:

writeParameters in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeConfidences

protected void writeConfidences(I object)
                         throws XMLStreamException

writeConfidences.

Specified by:

writeConfidences in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeNegative

protected void writeNegative(I object)
                      throws XMLStreamException

writeNegative.

Specified by:

writeNegative in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeAvailabilityRef

protected void writeAvailabilityRef(String availability)
                             throws XMLStreamException

writeAvailabilityRef.

Parameters:

availability - a String object.

Throws:

XMLStreamException - if any.

writeAvailabilityDescription

protected void writeAvailabilityDescription(String availability)
                                     throws XMLStreamException

writeAvailabilityDescription.

Parameters:

availability - a String object.

Throws:

XMLStreamException - if any.

writeInferredInteractions

protected void writeInferredInteractions(I object)
                                  throws XMLStreamException

writeInferredInteractions.

Specified by:

writeInferredInteractions in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a I object.

Throws:

XMLStreamException - if any.

writeStartInteraction

protected void writeStartInteraction()
                              throws XMLStreamException

writeStartInteraction.

Specified by:

writeStartInteraction in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Throws:

XMLStreamException - if any.