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

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.xml25.AbstractXmlModelledInteractionWriter<I>

All Implemented Interfaces:

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

Direct Known Subclasses:

XmlComplexWriter, XmlComplexWriter, XmlModelledBinaryInteractionWriter, XmlModelledBinaryInteractionWriter, XmlModelledInteractionWriter, XmlModelledInteractionWriter

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

Abstract class for XML 2.5 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
Experiment	extractDefaultExperimentFrom(I interaction)	extractDefaultExperimentFrom.
List<Experiment>	extractDefaultExperimentsFrom(I interaction)	extractDefaultExperimentsFrom.
PsiXmlElementWriter<AbstractInferredInteraction>	getXmlInferredInteractionWriter()	getXmlInferredInteractionWriter.
protected void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseDefaultExperiment()	initialiseDefaultExperiment.
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseParameterWriter()	initialiseParameterWriter.
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	setXmlInferredInteractionWriter(PsiXmlElementWriter<AbstractInferredInteraction> inferredInteractionWriter)	setXmlInferredInteractionWriter.
protected void	writeCooperativeEffect(I object, boolean startAttributeList)	writeCooperativeEffect.
protected void	writeCooperativeEffectAttribute(String name, String nameAc, String value)	writeCooperativeEffectAttribute.
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	writeOtherProperties(I object)	writeOtherProperties.
protected void	writeStartInteraction()	writeStartInteraction.

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

getDefaultExperiments, initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseXrefWriter, setDefaultExperiments, writeIntraMolecular

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

getAliasWriter, getConfidenceWriter, getParameterWriter, setAliasWriter, setConfidenceWriter, 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, 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, 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.PsiXmlExtendedInteractionWriter

getDefaultExperiments, setDefaultExperiments

Methods inherited from interface psidev.psi.mi.jami.xml.io.writer.elements.PsiXmlInteractionWriter

getDefaultExperiment, setComplexAsInteractor, writeComplexAsInteractor

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

getXmlInferredInteractionWriter

public PsiXmlElementWriter<AbstractInferredInteraction> getXmlInferredInteractionWriter()

getXmlInferredInteractionWriter.

Returns:

a PsiXmlElementWriter object.

setXmlInferredInteractionWriter

public void setXmlInferredInteractionWriter(PsiXmlElementWriter<AbstractInferredInteraction> inferredInteractionWriter)

setXmlInferredInteractionWriter.

Parameters:

inferredInteractionWriter - a PsiXmlElementWriter object.

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>

initialiseDefaultExperiment

protected void initialiseDefaultExperiment()

initialiseDefaultExperiment.

Overrides:

initialiseDefaultExperiment in class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

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 AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>

Parameters:

defaultExperiment - : default experiment

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

extractDefaultExperimentFrom

public Experiment extractDefaultExperimentFrom(I interaction)

extractDefaultExperimentFrom.

Specified by:

extractDefaultExperimentFrom in interface PsiXmlInteractionWriter<I extends ModelledInteraction>

Overrides:

extractDefaultExperimentFrom in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

interaction - a T object.

Returns:

the default experiment for this interaction

writeInteractionType

protected void writeInteractionType(I object)
                             throws XMLStreamException

writeInteractionType.

Overrides:

writeInteractionType in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.

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.

writeInferredInteractions

protected void writeInferredInteractions(I object)
                                  throws XMLStreamException

writeInferredInteractions.

Specified by:

writeInferredInteractions in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a I object.

Throws:

XMLStreamException - if any.

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.

writeCooperativeEffectAttribute

protected void writeCooperativeEffectAttribute(String name,
                                               String nameAc,
                                               String value)
                                        throws XMLStreamException

writeCooperativeEffectAttribute.

Parameters:

name - a String object.

nameAc - a String object.

value - a String object.

Throws:

XMLStreamException - if any.

writeOtherProperties

protected void writeOtherProperties(I object)

writeOtherProperties.

Specified by:

writeOtherProperties in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

writeStartInteraction

protected void writeStartInteraction()
                              throws XMLStreamException

writeStartInteraction.

Specified by:

writeStartInteraction in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Throws:

XMLStreamException - if any.