Package psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25

Class AbstractXmlInteractionWriter<I extends Interaction>

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlInteractionWriter<T,Participant>

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25.AbstractXmlInteractionWriter<I>

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.AbstractXmlInteractionWriter<I>

All Implemented Interfaces:

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

Direct Known Subclasses:

XmlBasicBinaryInteractionWriter, XmlBasicBinaryInteractionWriter, XmlBasicInteractionWriter, XmlBasicInteractionWriter

public abstract class AbstractXmlInteractionWriter<I extends Interaction>
extends AbstractXmlInteractionWriter<I>
implements PsiXmlExtendedInteractionWriter<I>

Abstract class for extended XML 2.5 interaction writer

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

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	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseInteractionTypeWriter()	initialiseInteractionTypeWriter.
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 void	writeInferredInteractions(I object)	writeInferredInteractions.
protected void	writeInteractionType(I object)	writeInteractionType.
protected void	writeIntraMolecular(I object)	writeIntraMolecular.
protected void	writeNames(I object)	writeNames.

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25.AbstractXmlInteractionWriter

initialiseInferredInteractionWriter, writeAvailability, writeConfidences, writeModelled, writeNegative, writeOtherAttributes, writeOtherProperties, writeParameters, writeStartInteraction

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

collectInferredInteractionsFrom, extractDefaultExperimentFrom, getAttributeWriter, getChecksumWriter, getDefaultExperiment, getExperimentWriter, getInferredInteractionWriter, getInteractionTypeWriter, getObjectIndex, getParticipantWriter, getStreamWriter, getVersion, getXrefWriter, initialiseDefaultExperiment, initialiseParticipantWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setDefaultExperiment, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeAttributes, writeComplexAsInteractor, writeExperiments, 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

AbstractXmlInteractionWriter

public AbstractXmlInteractionWriter(PsiXmlVersion version,
                                    XMLStreamWriter writer,
                                    PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlInteractionWriter.

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 Interaction>

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 Interaction>

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.

extractDefaultExperimentsFrom

public List<Experiment> extractDefaultExperimentsFrom(I interaction)

extractDefaultExperimentsFrom.

Specified by:

extractDefaultExperimentsFrom in interface PsiXmlExtendedInteractionWriter<I extends Interaction>

Parameters:

interaction - a T object.

Returns:

the default experiments for this interaction

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.

initialiseInteractionTypeWriter

protected void initialiseInteractionTypeWriter()

initialiseInteractionTypeWriter.

Overrides:

initialiseInteractionTypeWriter in class AbstractXmlInteractionWriter<I extends Interaction>

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Overrides:

initialiseXrefWriter in class AbstractXmlInteractionWriter<I extends Interaction>

writeNames

protected void writeNames(I object)
                   throws XMLStreamException

writeNames.

Overrides:

writeNames in class AbstractXmlInteractionWriter<I extends Interaction,Participant>

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 Interaction>

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 Interaction,Participant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeInferredInteractions

protected void writeInferredInteractions(I object)
                                  throws XMLStreamException

writeInferredInteractions.

Overrides:

writeInferredInteractions in class AbstractXmlInteractionWriter<I extends Interaction>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Overrides:

initialiseExperimentWriter in class AbstractXmlInteractionWriter<I extends Interaction>

writeExperimentRef

protected CvTerm writeExperimentRef()
                             throws XMLStreamException

writeExperimentRef.

Overrides:

writeExperimentRef in class AbstractXmlInteractionWriter<I extends Interaction,Participant>

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperimentDescription

protected CvTerm writeExperimentDescription()
                                     throws XMLStreamException

writeExperimentDescription.

Overrides:

writeExperimentDescription in class AbstractXmlInteractionWriter<I extends Interaction,Participant>

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.