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

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.extended.AbstractXmlInteractionEvidenceWriter<I>

All Implemented Interfaces:

PsiXmlElementWriter<I>, PsiXmlExtendedInteractionWriter<I>, PsiXmlInteractionWriter<I>

Direct Known Subclasses:

AbstractXmlInteractionEvidenceWriter, AbstractXmlInteractionEvidenceWriter

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

Abstract class for interaction evidence writers that write expanded interactions (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
AbstractXmlInteractionEvidenceWriter(PsiXmlVersion version, XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for AbstractXmlInteractionEvidenceWriter.

Method Summary

Modifier and Type	Method	Description
List<Experiment>	extractDefaultExperimentsFrom(I interaction)	extractDefaultExperimentsFrom.
PsiXmlElementWriter<Alias>	getAliasWriter()	Getter for the field aliasWriter.
List<Experiment>	getDefaultExperiments()	The default experiments that will be used to write a valid XML file but are not real experiments attached to the interaction.
PsiXmlElementWriter<AbstractInferredInteraction>	getXmlInferredInteractionWriter()	getXmlInferredInteractionWriter.
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	setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
void	setDefaultExperiments(List<Experiment> exp)	Sets the default experiments that will be used to write a valid XML file even if the interaction does not have any valid experiment
void	setXmlInferredInteractionWriter(PsiXmlElementWriter<AbstractInferredInteraction> inferredInteractionWriter)	setXmlInferredInteractionWriter.
protected CvTerm	writeExperimentDescription()	writeExperimentDescription.
protected CvTerm	writeExperimentRef()	writeExperimentRef.
protected CvTerm	writeExperiments(I object)	writeExperiments.
protected void	writeInferredInteractions(I object)	writeInferredInteractions.
protected void	writeInteractionType(I object)	writeInteractionType.
protected void	writeIntraMolecular(I object)	writeIntraMolecular.
protected void	writeModelled(I object)	writeModelled.
protected void	writeNames(I object)	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, initialiseParticipantWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeAttributes, writeAvailability, writeComplexAsInteractor, writeOtherProperties, 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

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

getDefaultExperiments

public List<Experiment> getDefaultExperiments()

The default experiments that will be used to write a valid XML file but are not real experiments attached to the interaction. It cannot be null.

Specified by:

getDefaultExperiments in interface PsiXmlExtendedInteractionWriter<I extends InteractionEvidence>

Returns:

a List object.

setDefaultExperiments

public void setDefaultExperiments(List<Experiment> exp)

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

Specified by:

setDefaultExperiments in interface PsiXmlExtendedInteractionWriter<I extends InteractionEvidence>

Parameters:

exp - a List object.

getXmlInferredInteractionWriter

public PsiXmlElementWriter<AbstractInferredInteraction> getXmlInferredInteractionWriter()

getXmlInferredInteractionWriter.

Returns:

a PsiXmlElementWriter object.

setXmlInferredInteractionWriter

public void setXmlInferredInteractionWriter(PsiXmlElementWriter<AbstractInferredInteraction> inferredInteractionWriter)

setXmlInferredInteractionWriter.

Parameters:

inferredInteractionWriter - a PsiXmlElementWriter object.

getAliasWriter

public PsiXmlElementWriter<Alias> getAliasWriter()

Getter for the field aliasWriter.

Returns:

a PsiXmlElementWriter object.

setAliasWriter

public void setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)

Setter for the field aliasWriter.

Parameters:

aliasWriter - a PsiXmlElementWriter object.

extractDefaultExperimentsFrom

public List<Experiment> extractDefaultExperimentsFrom(I interaction)

extractDefaultExperimentsFrom.

Specified by:

extractDefaultExperimentsFrom in interface PsiXmlExtendedInteractionWriter<I extends InteractionEvidence>

Parameters:

interaction - a T object.

Returns:

the default experiments for this interaction

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>

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>

writeNames

protected void writeNames(I object)
                   throws XMLStreamException

writeNames.

Overrides:

writeNames in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeIntraMolecular

protected void writeIntraMolecular(I object)
                            throws XMLStreamException

writeIntraMolecular.

Overrides:

writeIntraMolecular 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.

Overrides:

writeModelled in class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeInteractionType

protected void writeInteractionType(I object)
                             throws XMLStreamException

writeInteractionType.

Overrides:

writeInteractionType in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeInferredInteractions

protected void writeInferredInteractions(I object)
                                  throws XMLStreamException

writeInferredInteractions.

Overrides:

writeInferredInteractions in class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

Parameters:

object - a I object.

Throws:

XMLStreamException - if any.

writeExperimentRef

protected CvTerm writeExperimentRef()
                             throws XMLStreamException

writeExperimentRef.

Overrides:

writeExperimentRef in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperimentDescription

protected CvTerm writeExperimentDescription()
                                     throws XMLStreamException

writeExperimentDescription.

Overrides:

writeExperimentDescription in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperiments

protected CvTerm writeExperiments(I object)
                           throws XMLStreamException

writeExperiments.

Overrides:

writeExperiments in class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.