public psidev.psi.mi.xml254.jaxb.Participant toJaxb(
psidev.psi.mi.xml.model.Participant mParticipant) throws ConverterException {
if (mParticipant == null) {
throw new IllegalArgumentException("You must give a non null model Participant.");
}
checkDependencies();
psidev.psi.mi.xml254.jaxb.Participant jParticipant =
new psidev.psi.mi.xml254.jaxb.Participant();
// Initialise the JAXB object reading the model
// 1. set attributes
jParticipant.setId(mParticipant.getId());
// 2. set sub elements
// interactor / interaction
if (mParticipant.hasInteractor() || mParticipant.hasInteractorRef()) {
// compact form: export ref
if (PsimiXmlForm.FORM_COMPACT
== ConverterContext.getInstance().getConverterConfig().getXmlForm()) {
if (mParticipant.hasInteractorRef())
jParticipant.setInteractorRef(mParticipant.getInteractorRef().getRef());
else jParticipant.setInteractorRef(mParticipant.getInteractor().getId());
}
// not compact form : export the full interactor
else {
jParticipant.setInteractor(interactorConverter.toJaxb(mParticipant.getInteractor()));
}
} else if (mParticipant.hasInteraction()) {
jParticipant.setInteractionRef(mParticipant.getInteraction().getId());
} else {
throw new ConverterException(
"Neither an interactor or an interaction was present in participant "
+ mParticipant.getId());
}
// BiologigicalRoles
if (mParticipant.hasBiologicalRole()) {
jParticipant.setBiologicalRole(cvTypeConverter.toJaxb(mParticipant.getBiologicalRole()));
}
// Names
if (mParticipant.hasNames()) {
jParticipant.setNames(namesConverter.toJaxb(mParticipant.getNames()));
}
// Xrefs
if (mParticipant.hasXref()) {
jParticipant.setXref(xrefConverter.toJaxb(mParticipant.getXref()));
}
// ConfidenceList
if (mParticipant.hasConfidences()) {
if (jParticipant.getConfidenceList() == null) {
jParticipant.setConfidenceList(new ConfidenceList());
}
for (psidev.psi.mi.xml.model.Confidence mConfidence : mParticipant.getConfidenceList()) {
jParticipant
.getConfidenceList()
.getConfidences()
.add(confidenceConverter.toJaxb(mConfidence));
}
}
// ExperimentalInteractor
if (mParticipant.hasExperimentalInteractors()) {
if (jParticipant.getExperimentalInteractorList() == null) {
jParticipant.setExperimentalInteractorList(
new psidev.psi.mi.xml254.jaxb.ExperimentalInteractorList());
}
for (ExperimentalInteractor mExperimentalInteractor :
mParticipant.getExperimentalInteractors()) {
jParticipant
.getExperimentalInteractorList()
.getExperimentalInteractors()
.add(experimentalInteractorConverter.toJaxb(mExperimentalInteractor));
}
}
// ExperimentalPreparations
if (mParticipant.hasExperimentalPreparations()) {
if (jParticipant.getExperimentalPreparationList() == null) {
jParticipant.setExperimentalPreparationList(
new psidev.psi.mi.xml254.jaxb.ExperimentalPreparationList());
}
for (ExperimentalPreparation mExperimentalPreparation :
mParticipant.getExperimentalPreparations()) {
jParticipant
.getExperimentalPreparationList()
.getExperimentalPreparations()
.add(experimentalPreparationConverter.toJaxb(mExperimentalPreparation));
}
}
// ExperimentalRoles
if (mParticipant.hasExperimentalRoles()) {
if (jParticipant.getExperimentalRoleList() == null) {
jParticipant.setExperimentalRoleList(new psidev.psi.mi.xml254.jaxb.ExperimentalRoleList());
}
for (ExperimentalRole mExperimentalRole : mParticipant.getExperimentalRoles()) {
jParticipant
.getExperimentalRoleList()
.getExperimentalRoles()
.add(experimentalRoleConverter.toJaxb(mExperimentalRole));
}
}
// Features
if (mParticipant.hasFeatures()) {
if (jParticipant.getFeatureList() == null) {
jParticipant.setFeatureList(new psidev.psi.mi.xml254.jaxb.FeatureList());
}
for (Feature mFeature : mParticipant.getFeatures()) {
jParticipant.getFeatureList().getFeatures().add(featureConverter.toJaxb(mFeature));
}
}
// HostOrganisms
if (!mParticipant.getHostOrganisms().isEmpty()) {
if (jParticipant.getHostOrganismList() == null) {
jParticipant.setHostOrganismList(new HostOrganismList());
}
for (HostOrganism mHostOrganism : mParticipant.getHostOrganisms()) {
jParticipant
.getHostOrganismList()
.getHostOrganisms()
.add(hostOrganismConverter.toJaxb(mHostOrganism));
}
}
// Parameters
if (mParticipant.hasParameters()) {
if (jParticipant.getParameterList() == null) {
jParticipant.setParameterList(new ParameterList());
}
for (Parameter mParameter : mParticipant.getParameters()) {
jParticipant.getParameterList().getParameters().add(parameterConverter.toJaxb(mParameter));
}
}
// ParticipantIdentificationMethod
if (mParticipant.hasParticipantIdentificationMethods()) {
if (jParticipant.getParticipantIdentificationMethodList() == null) {
jParticipant.setParticipantIdentificationMethodList(
new psidev.psi.mi.xml254.jaxb.ParticipantIdentificationMethodList());
}
for (ParticipantIdentificationMethod mParticipantIdentificationMethod :
mParticipant.getParticipantIdentificationMethods()) {
jParticipant
.getParticipantIdentificationMethodList()
.getParticipantIdentificationMethods()
.add(participantIdentificationMethodConverter.toJaxb(mParticipantIdentificationMethod));
}
}
// Attributes
if (mParticipant.hasAttributes()) {
if (jParticipant.getAttributeList() == null) {
jParticipant.setAttributeList(new AttributeList());
}
for (Attribute mAttribute : mParticipant.getAttributes()) {
jParticipant.getAttributeList().getAttributes().add(attributeConverter.toJaxb(mAttribute));
}
}
return jParticipant;
}
