public Names getNames() { return organism.getNames(); }
name = getName(organism.getNames());
String shortLabel = o.getNames().getShortLabel(); if (shortLabel != null) { organismXrefs.add(new CrossReferenceImpl("taxid", taxId, shortLabel)); String fullName = o.getNames().getFullName(); if (fullName != null && !shortLabel.equalsIgnoreCase(fullName)) { organismXrefs.add(new CrossReferenceImpl("taxid", taxId, fullName));
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.setNames( namesConverter.toJaxb( mOrganism.getNames() ) );
jOrganism.setNames( namesConverter.toJaxb( mOrganism.getNames() ) );
HostOrganism hostOrganism = new HostOrganism(); hostOrganism.setNcbiTaxId(organism.getNcbiTaxId()); hostOrganism.setNames(organism.getNames()); hostOrganism.setCellType(organism.getCellType()); hostOrganism.setCompartment(organism.getCompartment());
if(org != null) { final Integer taxID = org.getNcbiTaxId(); mapNames(nodeTable, node.getSUID(), org.getNames(), "Species ");