Package psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.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.abstracts.xml25.AbstractXmlModelledInteractionWriter<I>

All Implemented Interfaces:

PsiXmlElementWriter<I>, PsiXmlInteractionWriter<I>

Direct Known Subclasses:

XmlComplexWriter, XmlComplexWriter, XmlModelledBinaryInteractionWriter, XmlModelledBinaryInteractionWriter, XmlModelledInteractionWriter, XmlModelledInteractionWriter

public abstract class AbstractXmlModelledInteractionWriter<I extends ModelledInteraction>
extends AbstractXmlModelledInteractionWriter<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.
protected void	initialiseConfidenceWriter()	initialiseConfidenceWriter.
protected void	initialiseDefaultExperiment()	initialiseDefaultExperiment.
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseInferredInteractionWriter()	initialiseInferredInteractionWriter.
protected void	initialiseInteractionTypeWriter()	initialiseInteractionTypeWriter.
protected void	initialiseParameterWriter()	initialiseParameterWriter.
protected void	initialiseXrefWriter()	initialiseXrefWriter.
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
protected void	writeCooperativeEffect(I object, boolean startAttributeList)	writeCooperativeEffect.
protected void	writeCooperativeEffectAttribute(String name, String nameAc, String value)	writeCooperativeEffectAttribute.
protected void	writeInferredInteractions(I object)	writeInferredInteractions.
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, setAliasWriter, setConfidenceWriter, setParameterWriter, writeAttributes, writeAvailability, writeConfidences, writeExperiments, 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, writeExperimentDescription, writeExperimentRef, 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(PsiXmlVersion version,
                                            XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlModelledInteractionWriter.

Parameters:

version - a PsiXmlVersion object.

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

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>

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>

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

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

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.