Package psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30

Class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlInteractionWriter<I,ParticipantEvidence>

psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.AbstractXmlInteractionEvidenceWriter<I>

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.AbstractXmlInteractionEvidenceWriter<I>

psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30.AbstractXmlInteractionEvidenceWriter<I>

All Implemented Interfaces:

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

Direct Known Subclasses:

XmlBinaryInteractionEvidenceWriter, XmlBinaryInteractionEvidenceWriter, XmlInteractionEvidenceWriter, XmlInteractionEvidenceWriter

public abstract class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>
extends AbstractXmlInteractionEvidenceWriter<I>

Abstract class for interaction evidence writers that write expanded interactions (having modelled, intramolecular properties, list of experiments, list of interaction types, etc.)

Since:

18/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractXmlInteractionEvidenceWriter(XMLStreamWriter writer, PsiXmlObjectCache objectIndex)	Constructor for AbstractXmlInteractionEvidenceWriter.

Method Summary

Modifier and Type	Method	Description
PsiXmlCausalRelationshipWriter	getCausalRelationshipWriter()	Getter for the field causalRelationshipWriter.
PsiXmlElementWriter<VariableParameterValueSet>	getVariableParameterValueSetWriter()	Getter for the field variableParameterValueSetWriter.
protected void	initialiseCausalRelationshipWriter()	initialiseCausalRelationshipWriter.
protected void	initialiseExperimentWriter()	initialiseExperimentWriter.
protected void	initialiseParameterWriter()	initialiseParameterWriter.
void	setCausalRelationshipWriter(PsiXmlCausalRelationshipWriter causalRelationshipWriter)	Setter for the field causalRelationshipWriter.
void	setVariableParameterValueSetWriter(PsiXmlElementWriter<VariableParameterValueSet> variableParameterValueSetWriter)	Setter for the field variableParameterValueSetWriter.
protected void	writeCausalRelationships(I object)	writeCausalRelationships.
protected void	writeExperimentalVariableValues(I object)	writeExperimentalVariableValues.
protected void	writeOtherProperties(I object)	writeOtherProperties.

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

extractDefaultExperimentsFrom, getAliasWriter, getDefaultExperiments, getXmlInferredInteractionWriter, initialiseConfidenceWriter, initialiseInferredInteractionWriter, initialiseInteractionTypeWriter, initialiseXrefWriter, setAliasWriter, setDefaultExperiments, setXmlInferredInteractionWriter, writeExperimentDescription, writeExperimentRef, writeExperiments, writeInferredInteractions, writeInteractionType, writeIntraMolecular, writeModelled, writeNames

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

extractDefaultExperimentFrom, getAvailabilityWriter, getConfidenceWriter, getParameterWriter, initialiseAvaliabilityWriter, initialiseDefaultExperiment, setAvailabilityWriter, setConfidenceWriter, setDefaultExperiment, setParameterWriter, writeAvailabilityDescription, writeAvailabilityRef, writeConfidences, writeNegative, writeOtherAttributes, writeParameters, writeStartInteraction

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, writeAttributes, writeAvailability, 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.PsiXmlInteractionWriter

extractDefaultExperimentFrom, getDefaultExperiment, setComplexAsInteractor, setDefaultExperiment, writeComplexAsInteractor

Constructor Detail

AbstractXmlInteractionEvidenceWriter

public AbstractXmlInteractionEvidenceWriter(XMLStreamWriter writer,
                                            PsiXmlObjectCache objectIndex)

Constructor for AbstractXmlInteractionEvidenceWriter.

Parameters:

writer - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Method Detail

getVariableParameterValueSetWriter

public PsiXmlElementWriter<VariableParameterValueSet> getVariableParameterValueSetWriter()

Getter for the field variableParameterValueSetWriter.

Returns:

a PsiXmlElementWriter object.

setVariableParameterValueSetWriter

public void setVariableParameterValueSetWriter(PsiXmlElementWriter<VariableParameterValueSet> variableParameterValueSetWriter)

Setter for the field variableParameterValueSetWriter.

Parameters:

variableParameterValueSetWriter - a PsiXmlElementWriter object.

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.

initialiseParameterWriter

protected void initialiseParameterWriter()

initialiseParameterWriter.

Overrides:

initialiseParameterWriter in class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

initialiseExperimentWriter

protected void initialiseExperimentWriter()

initialiseExperimentWriter.

Overrides:

initialiseExperimentWriter in class AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence>

writeOtherProperties

protected void writeOtherProperties(I object)
                             throws XMLStreamException

writeOtherProperties.

Specified by:

writeOtherProperties in class AbstractXmlInteractionWriter<I extends InteractionEvidence,ParticipantEvidence>

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.

writeExperimentalVariableValues

protected void writeExperimentalVariableValues(I object)
                                        throws XMLStreamException

writeExperimentalVariableValues.

Parameters:

object - a I object.

Throws:

XMLStreamException - if any.