/**
* 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 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++;
}
/**
* Gets the Interaction Participant List.
*
* @param interaction Interaction object.
* @return Castor Participant List.
*/
private InteractionElementType.ParticipantList getParticipantList(
org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
InteractionElementType.ParticipantList participantList =
new InteractionElementType.ParticipantList();
List interactors = interaction.getInteractors();
for (int i = 0; i < interactors.size(); i++) {
Interactor interactor = (Interactor) interactors.get(i);
String name = interactor.getName();
ParticipantType participant1 = createParticipant(name);
participantList.getParticipant().add(participant1);
}
return participantList;
}
/**
* Conditionally adds Protein to HashMap.
*
* @param interactor Interactor Object.
* @param interactorMap HashMap of NonRedundant Interactors.
*/
private void addToHashMap(Interactor interactor, HashMap interactorMap) {
String orfName = interactor.getName();
if (!interactorMap.containsKey(orfName)) {
interactorMap.put(orfName, interactor);
}
}
/** Sets Sequence Data. */
private void setSequence(Interactor interactor, InteractorElementType jaxbInteractor) {
String seqData = (String) interactor.getAttribute(InteractorVocab.SEQUENCE_DATA);
if (seqData != null) {
jaxbInteractor.setSequence(seqData);
}
}