/**
* Gets Interactor List.
*
* @return Castor InteractorList.
*/
private EntrySet.Entry.InteractorList getInteractorList() {
HashMap proteinSet = getNonRedundantInteractors();
EntrySet.Entry.InteractorList interactorList = new EntrySet.Entry.InteractorList();
// Iterate through all Interactors
Iterator iterator = proteinSet.values().iterator();
while (iterator.hasNext()) {
// Create new Interactor
Interactor interactor = (Interactor) iterator.next();
InteractorElementType jaxbInteractor = new InteractorElementType();
setNameId(interactor, jaxbInteractor);
setOrganism(interactor, jaxbInteractor);
setSequence(interactor, jaxbInteractor);
XrefType xref = createExternalRefs(interactor);
if (xref != null) {
jaxbInteractor.setXref(xref);
}
// Add to Interactor List
interactorList.getInteractor().add(jaxbInteractor);
}
return interactorList;
}
/**
* 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++;
}
/**
* 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);
}
/** Sets Sequence Data. */
private void setSequence(Interactor interactor, InteractorElementType jaxbInteractor) {
String seqData = (String) interactor.getAttribute(InteractorVocab.SEQUENCE_DATA);
if (seqData != null) {
jaxbInteractor.setSequence(seqData);
}
}
