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

Class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

java.lang.Object

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

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

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

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30.AbstractXmlModelledInteractionWriter<I>

All Implemented Interfaces:

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

Direct Known Subclasses:

XmlModelledBinaryInteractionWriter, XmlModelledBinaryInteractionWriter, XmlModelledInteractionWriter, XmlModelledInteractionWriter

public abstract class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>
extends AbstractXmlModelledInteractionWriter<I>
implements PsiXmlExtendedInteractionWriter<I>

Abstract class for XML 3.0 writers of modelled interaction

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
List<Experiment>	extractDefaultExperimentsFrom(I interaction)	extractDefaultExperimentsFrom.
PsiXmlElementWriter<Allostery>	getAllosteryWriter()	Getter for the field allosteryWriter.
PsiXmlElementWriter<Set<Feature>>	getBindingFeaturesWriter()	Getter for the field bindingFeaturesWriter.
PsiXmlCausalRelationshipWriter	getCausalRelationshipWriter()	Getter for the field causalRelationshipWriter.
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<Organism>	getOrganismWriter()	Getter for the field organismWriter.
PsiXmlElementWriter<Preassembly>	getPreAssemblyWriter()	Getter for the field preAssemblyWriter.
protected void	initialiseCausalRelationshipWriter()	initialiseCausalRelationshipWriter.
protected void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseParameterWriter()	initialiseParameterWriter.
void	setAllosteryWriter(PsiXmlElementWriter<Allostery> allosteryWriter)	Setter for the field allosteryWriter.
void	setBindingFeaturesWriter(PsiXmlElementWriter<Set<Feature>> bindingFeaturesWriter)	Setter for the field bindingFeaturesWriter.
void	setCausalRelationshipWriter(PsiXmlCausalRelationshipWriter causalRelationshipWriter)	Setter for the field causalRelationshipWriter.
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	setOrganismWriter(PsiXmlElementWriter<Organism> organismWriter)	Setter for the field organismWriter.
void	setPreAssemblyWriter(PsiXmlElementWriter<Preassembly> preAssemblyWriter)	Setter for the field preAssemblyWriter.
protected void	writeCausalRelationships(I object)	writeCausalRelationships.
protected void	writeCooperativeEffect(I object, boolean startAttributeList)	writeCooperativeEffect.
protected void	writeCooperativeEffects(I object)	writeCooperativeEffects.
protected void	writeEvidenceType(I object)	writeEvidenceType.
protected CvTerm	writeExperimentDescription()	writeExperimentDescription.
protected CvTerm	writeExperimentRef()	writeExperimentRef.
protected CvTerm	writeExperiments(I object)	writeExperiments.
protected void	writeInferredInteractions(I object)	writeInferredInteractions.
protected void	writeInteractorType(Complex complex)	writeInteractorType.
protected void	writeIntraMolecular(I object)	writeIntraMolecular.
protected void	writeOrganism(Complex complex)	writeOrganism.
protected void	writeOtherProperties(I object)	writeOtherProperties.
protected void	writeStartInteraction()	writeStartInteraction.

Methods inherited from class psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.AbstractXmlModelledInteractionWriter

initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseXrefWriter

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

getAliasWriter, getConfidenceWriter, getParameterWriter, initialiseDefaultExperiment, setAliasWriter, setConfidenceWriter, setDefaultExperiment, setParameterWriter, writeAttributes, writeAvailability, writeConfidences, writeModelled, writeNames, writeNegative, writeOtherAttributes, writeParameters

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, initialiseParticipantWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeComplexAsInteractor, writeInteractionType, 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

AbstractXmlModelledInteractionWriter

public AbstractXmlModelledInteractionWriter(XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlModelledInteractionWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

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.

getPreAssemblyWriter

public PsiXmlElementWriter<Preassembly> getPreAssemblyWriter()

Getter for the field preAssemblyWriter.

Returns:

a PsiXmlElementWriter object.

setPreAssemblyWriter

public void setPreAssemblyWriter(PsiXmlElementWriter<Preassembly> preAssemblyWriter)

Setter for the field preAssemblyWriter.

Parameters:

preAssemblyWriter - a PsiXmlElementWriter object.

getAllosteryWriter

public PsiXmlElementWriter<Allostery> getAllosteryWriter()

Getter for the field allosteryWriter.

Returns:

a PsiXmlElementWriter object.

setAllosteryWriter

public void setAllosteryWriter(PsiXmlElementWriter<Allostery> allosteryWriter)

Setter for the field allosteryWriter.

Parameters:

allosteryWriter - a PsiXmlElementWriter object.

getOrganismWriter

public PsiXmlElementWriter<Organism> getOrganismWriter()

Getter for the field organismWriter.

Returns:

a PsiXmlElementWriter object.

setOrganismWriter

public void setOrganismWriter(PsiXmlElementWriter<Organism> organismWriter)

Setter for the field organismWriter.

Parameters:

organismWriter - a PsiXmlElementWriter object.

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 ModelledInteraction>

Overrides:

getDefaultExperiments in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

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 ModelledInteraction>

Overrides:

setDefaultExperiments in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

Parameters:

exp - a List object.

getBindingFeaturesWriter

public PsiXmlElementWriter<Set<Feature>> getBindingFeaturesWriter()

Getter for the field bindingFeaturesWriter.

Returns:

a PsiXmlElementWriter object.

setBindingFeaturesWriter

public void setBindingFeaturesWriter(PsiXmlElementWriter<Set<Feature>> bindingFeaturesWriter)

Setter for the field bindingFeaturesWriter.

Parameters:

bindingFeaturesWriter - a PsiXmlElementWriter object.

extractDefaultExperimentsFrom

public List<Experiment> extractDefaultExperimentsFrom(I interaction)

extractDefaultExperimentsFrom.

Specified by:

extractDefaultExperimentsFrom in interface PsiXmlExtendedInteractionWriter<I extends ModelledInteraction>

Parameters:

interaction - a T object.

Returns:

the default experiments for this interaction

writeCooperativeEffect

protected void writeCooperativeEffect(I object,
                                      boolean startAttributeList)
                               throws XMLStreamException

writeCooperativeEffect.

Specified by:

writeCooperativeEffect in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

Parameters:

object - a I object.

startAttributeList - a boolean.

Throws:

XMLStreamException - if any.

writeInferredInteractions

protected void writeInferredInteractions(I object)
                                  throws XMLStreamException

writeInferredInteractions.

Specified by:

writeInferredInteractions in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Overrides:

initialiseExperimentWriter in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

initialiseConfidenceWriter

protected void initialiseConfidenceWriter()

initialiseConfidenceWriter.

Specified by:

initialiseConfidenceWriter in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

initialiseParameterWriter

protected void initialiseParameterWriter()

initialiseParameterWriter.

Specified by:

initialiseParameterWriter in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

writeExperimentRef

protected CvTerm writeExperimentRef()
                             throws XMLStreamException

writeExperimentRef.

Overrides:

writeExperimentRef in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperimentDescription

protected CvTerm writeExperimentDescription()
                                     throws XMLStreamException

writeExperimentDescription.

Overrides:

writeExperimentDescription in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeExperiments

protected CvTerm writeExperiments(I object)
                           throws XMLStreamException

writeExperiments.

Overrides:

writeExperiments in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeIntraMolecular

protected void writeIntraMolecular(I object)
                            throws XMLStreamException

writeIntraMolecular.

Overrides:

writeIntraMolecular in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeOtherProperties

protected void writeOtherProperties(I object)
                             throws XMLStreamException

writeOtherProperties.

Specified by:

writeOtherProperties in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

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.

writeCooperativeEffects

protected void writeCooperativeEffects(I object)
                                throws XMLStreamException

writeCooperativeEffects.

Parameters:

object - a I object.

Throws:

XMLStreamException - if any.

writeEvidenceType

protected void writeEvidenceType(I object)

writeEvidenceType.

Parameters:

object - a I object.

writeInteractorType

protected void writeInteractorType(Complex complex)

writeInteractorType.

Parameters:

complex - a Complex object.

writeOrganism

protected void writeOrganism(Complex complex)

writeOrganism.

Parameters:

complex - a Complex object.

writeStartInteraction

protected void writeStartInteraction()
                              throws XMLStreamException

writeStartInteraction.

Specified by:

writeStartInteraction in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Throws:

XMLStreamException - if any.