/**
* Sets Interactor Organism.
*
* @param interactor Data Services Interactor Object.
* @param jaxbInteractor JAXB Protein Interactor Object.
*/
private void setOrganism(Interactor interactor, InteractorElementType jaxbInteractor) {
InteractorElementType.Organism organism = new InteractorElementType.Organism();
String taxonomyID = (String) interactor.getAttribute(InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID);
if (taxonomyID != null) {
int taxId = Integer.parseInt(taxonomyID);
organism.setNcbiTaxId(taxId);
}
NamesType orgNames = new NamesType();
String commonName = (String) interactor.getAttribute(InteractorVocab.ORGANISM_COMMON_NAME);
if (commonName != null) {
orgNames.setShortLabel(commonName);
}
String speciesName = (String) interactor.getAttribute(InteractorVocab.ORGANISM_SPECIES_NAME);
if (speciesName != null) {
orgNames.setFullName(speciesName);
}
organism.setNames(orgNames);
jaxbInteractor.setOrganism(organism);
}
/**
* Creates a new Names Object.
*
* @param shortLabel Short Name Label.
* @param fullName Full Name/Description.
* @return Castor Names Object.
*/
private NamesType createName(String shortLabel, String fullName) {
NamesType names = new NamesType();
names.setShortLabel(shortLabel);
if (fullName != null) {
names.setFullName(fullName);
}
return names;
}
/**
* Sets Interactor Name and ID.
*
* @param interactor Data Services Interactor object.
* @param jaxbInteractor JAXB Protein Interactor Object.
*/
private void setNameId(Interactor interactor, InteractorElementType jaxbInteractor) {
NamesType names = new NamesType();
names.setShortLabel(interactor.getName());
String fullName = (String) interactor.getAttribute(InteractorVocab.FULL_NAME);
if (fullName != null) {
names.setFullName(fullName);
}
jaxbInteractor.setNames(names);
jaxbInteractor.setId(interactorId);
interactorMap.put(interactor.getName(), interactorId);
interactorId++;
}
