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

All Implemented Interfaces:

PsiXmlElementWriter<I>, PsiXmlInteractionWriter<I>

Direct Known Subclasses:

XmlModelledBinaryInteractionWriter, XmlModelledBinaryInteractionWriter, XmlModelledInteractionWriter, XmlModelledInteractionWriter

public abstract class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>
extends AbstractXmlModelledInteractionWriter<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
PsiXmlElementWriter<Allostery>	getAllosteryWriter()	Getter for the field allosteryWriter.
PsiXmlElementWriter<Set<Feature>>	getBindingFeaturesWriter()	Getter for the field bindingFeaturesWriter.
PsiXmlCausalRelationshipWriter	getCausalRelationshipWriter()	Getter for the field causalRelationshipWriter.
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	initialiseInferredInteractionWriter()	initialiseInferredInteractionWriter.
protected void	initialiseInteractionTypeWriter()	initialiseInteractionTypeWriter.
protected void	initialiseParameterWriter()	initialiseParameterWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
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	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	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.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, writeIntraMolecular, writeParticipants, writeXref, writeXrefFromInteractionIdentifiers, writeXrefFromInteractionXrefs

Methods inherited from class java.lang.Object

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

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.

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.

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.

initialiseInferredInteractionWriter

protected void initialiseInferredInteractionWriter()

initialiseInferredInteractionWriter.

Specified by:

initialiseInferredInteractionWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Specified by:

initialiseXrefWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Specified by:

initialiseExperimentWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

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>

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.

initialiseInteractionTypeWriter

protected void initialiseInteractionTypeWriter()

initialiseInteractionTypeWriter.

Specified by:

initialiseInteractionTypeWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

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.

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.

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.

writeStartInteraction

protected void writeStartInteraction()
                              throws XMLStreamException

writeStartInteraction.

Specified by:

writeStartInteraction in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Throws:

XMLStreamException - if any.