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

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>

All Implemented Interfaces:

PsiXmlElementWriter<I>, PsiXmlInteractionWriter<I>

Direct Known Subclasses:

AbstractXmlModelledInteractionWriter, AbstractXmlModelledInteractionWriter, AbstractXmlModelledInteractionWriter

public abstract class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>
extends AbstractXmlInteractionWriter<I,ModelledParticipant>

Abstract class for XML writers of modelled interaction

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
PsiXmlElementWriter<Alias>	getAliasWriter()	Getter for the field aliasWriter.
PsiXmlElementWriter<Confidence>	getConfidenceWriter()	Getter for the field confidenceWriter.
PsiXmlParameterWriter	getParameterWriter()	Getter for the field parameterWriter.
protected abstract void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseDefaultExperiment()	initialiseDefaultExperiment.
protected abstract void	initialiseParameterWriter()	initialiseParameterWriter.
void	setAliasWriter(PsiXmlElementWriter<Alias> aliasWriter)	Setter for the field aliasWriter.
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	writeAttributes(I object)	writeAttributes.
protected void	writeAvailability(I object)	writeAvailability.
protected void	writeConfidences(I object)	writeConfidences.
protected abstract void	writeCooperativeEffect(I object, boolean startAttributeList)	writeCooperativeEffect.
protected CvTerm	writeExperiments(I object)	writeExperiments.
protected void	writeModelled(I object)	writeModelled.
protected void	writeNames(I object)	writeNames.
protected void	writeNegative(I object)	writeNegative.
protected void	writeOtherAttributes(I object)	writeOtherAttributes.
protected void	writeParameters(I object)	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, initialiseExperimentWriter, initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseParticipantWriter, initialiseXrefWriter, newExperiment, newPublication, newPublication, newXmlCvTerm, setAttributeWriter, setChecksumWriter, setComplexAsInteractor, setExperimentWriter, setInferredInteractionWriter, setInteractionTypeWriter, setParticipantWriter, setXrefWriter, write, writeAttribute, writeComplexAsInteractor, writeExperimentDescription, writeExperimentRef, writeInferredInteractions, writeInteractionType, writeIntraMolecular, writeOtherProperties, writeParticipants, writeStartInteraction, 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(PsiXmlVersion version,
                                            XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlModelledInteractionWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getConfidenceWriter

public PsiXmlElementWriter<Confidence> getConfidenceWriter()

Getter for the field confidenceWriter.

Returns:

a PsiXmlElementWriter object.

initialiseConfidenceWriter

protected abstract void initialiseConfidenceWriter()

initialiseConfidenceWriter.

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.

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 ModelledInteraction,ModelledParticipant>

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 ModelledInteraction>

Overrides:

setDefaultExperiment in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

defaultExperiment - : default experiment

writeAvailability

protected void writeAvailability(I object)

writeAvailability.

Specified by:

writeAvailability in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

writeOtherAttributes

protected void writeOtherAttributes(I object)

writeOtherAttributes.

Specified by:

writeOtherAttributes in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

writeModelled

protected void writeModelled(I object)

writeModelled.

Specified by:

writeModelled in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

writeParameters

protected void writeParameters(I object)
                        throws XMLStreamException

writeParameters.

Specified by:

writeParameters in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

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 ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeAttributes

protected void writeAttributes(I object)
                        throws XMLStreamException

writeAttributes.

Overrides:

writeAttributes in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

writeCooperativeEffect

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

writeCooperativeEffect.

Parameters:

object - a I object.

startAttributeList - a boolean.

Throws:

XMLStreamException - if any.

writeNegative

protected void writeNegative(I object)

writeNegative.

Specified by:

writeNegative in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

writeExperiments

protected CvTerm writeExperiments(I object)
                           throws XMLStreamException

writeExperiments.

Specified by:

writeExperiments in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

Returns:

a CvTerm object.

Throws:

XMLStreamException - if any.

writeNames

protected void writeNames(I object)
                   throws XMLStreamException

writeNames.

Overrides:

writeNames in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.