@Override protected Interactor newIntactObjectInstance( psidev.psi.mi.xml.model.Interactor psiObject ) { String shortLabel = psiObject.getNames().getShortLabel(); return newInteractorAccordingToType( psiObject.getOrganism(), shortLabel, psiObject.getInteractorType() ); }
private BioSource getBioSource(Interactor interactor) { Organism organism = interactor.getOrganism();
psidev.psi.mi.xml.model.Organism o = xmlInteractor.getOrganism(); List<CrossReference> organismXrefs = new ArrayList<CrossReference>(); String taxId = String.valueOf(o.getNcbiTaxId());
if((interactor.hasOrganism() && interactor.getOrganism().hasCompartment())) { cellularLocation = findOrCreateControlledVocabulary( interactor.getOrganism().getCompartment(), CellularLocationVocabulary.class);
jInteractor.setOrganism( organismConverter.toJaxb( mInteractor.getOrganism(), psidev.psi.mi.xml254.jaxb.Interactor.Organism.class ) );
jInteractor.setOrganism( organismConverter.toJaxb( mInteractor.getOrganism(), InteractorElementType.Organism.class ) );
Organism organism = psiObject.getOrganism();
nodeTable.getRow(node.getSUID()).set(INTERACTOR_TYPE, shortName); final Organism org = interactor.getOrganism(); if(org != null) { final Integer taxID = org.getNcbiTaxId();