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

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>

All Implemented Interfaces:

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

Direct Known Subclasses:

AbstractXmlModelledInteractionWriter, AbstractXmlModelledInteractionWriter

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

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
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.
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseInferredInteractionWriter()	initialiseInferredInteractionWriter.
protected void	initialiseInteractionTypeWriter()	initialiseInteractionTypeWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
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
protected void	writeIntraMolecular(I object)	writeIntraMolecular.

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

getAliasWriter, getConfidenceWriter, getParameterWriter, initialiseConfidenceWriter, initialiseDefaultExperiment, initialiseParameterWriter, setAliasWriter, setConfidenceWriter, setDefaultExperiment, setParameterWriter, writeAttributes, writeAvailability, writeConfidences, writeCooperativeEffect, writeExperiments, 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, writeExperimentDescription, writeExperimentRef, writeInferredInteractions, writeInteractionType, writeOtherProperties, writeParticipants, writeStartInteraction, 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

extractDefaultExperimentsFrom

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

extractDefaultExperimentFrom, getDefaultExperiment, setComplexAsInteractor, setDefaultExperiment, 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

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>

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>

Parameters:

exp - a List object.

initialiseXrefWriter

protected void initialiseXrefWriter()

initialiseXrefWriter.

Specified by:

initialiseXrefWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

initialiseInferredInteractionWriter

protected void initialiseInferredInteractionWriter()

initialiseInferredInteractionWriter.

Specified by:

initialiseInferredInteractionWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

initialiseInteractionTypeWriter

protected void initialiseInteractionTypeWriter()

initialiseInteractionTypeWriter.

Specified by:

initialiseInteractionTypeWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Specified by:

initialiseExperimentWriter in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

writeIntraMolecular

protected void writeIntraMolecular(I object)
                            throws XMLStreamException

writeIntraMolecular.

Overrides:

writeIntraMolecular in class AbstractXmlInteractionWriter<I extends ModelledInteraction,ModelledParticipant>

Parameters:

object - a T object.

Throws:

XMLStreamException - if any.