/** * Check if the optional compartment is defined. * * @return true if defined, false otherwise. */ public boolean hasCompartment() { return organism.getCompartment() != null; }
public Compartment getCompartment() { return organism.getCompartment(); }
if((interactor.hasOrganism() && interactor.getOrganism().hasCompartment())) { cellularLocation = findOrCreateControlledVocabulary( interactor.getOrganism().getCompartment(), CellularLocationVocabulary.class);
public BioSource psiToIntact(Organism psiObject) { if (psiObject == null) return null; psiStartConversion(psiObject); int taxId = psiObject.getNcbiTaxId(); BioSource bioSource = new BioSource(); bioSource.setTaxId(String.valueOf(taxId)); bioSource.setOwner(getInstitution()); IntactConverterUtils.populateNames(psiObject.getNames(), bioSource, aliasConverter); // cell type final CellType cellType = psiObject.getCellType(); if (cellType != null) { CvCellType intactCellType = cellTypeConverter.psiToIntact(cellType); bioSource.setCvCellType(intactCellType); } // tissue final Tissue tissue = psiObject.getTissue(); if (tissue != null) { CvTissue intactTissue = tissueConverter.psiToIntact(tissue); bioSource.setCvTissue(intactTissue); } if (psiObject.getCompartment() != null){ log.warn("Organism having a compartment : "+psiObject.getNcbiTaxId()+". Compartment is not converted in IntAct and is ignored."); } psiEndConversion(psiObject); return bioSource; }
jOrganism.setCompartment( openCvTypeConverter.toJaxb( mOrganism.getCompartment() ) );
jOrganism.setCompartment( openCvTypeConverter.toJaxb( mOrganism.getCompartment() ) );
hostOrganism.setNames(organism.getNames()); hostOrganism.setCellType(organism.getCellType()); hostOrganism.setCompartment(organism.getCompartment()); hostOrganism.setTissue(organism.getTissue());