private void synchronizeBioSource( BioSource bioSource, boolean synchronizeAnnotatedAttributes ) { bioSource.setCvCellType( synchronize( bioSource.getCvCellType() ) ); bioSource.setCvTissue( synchronize( bioSource.getCvTissue() ) ); if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( bioSource ); } }
private void synchronizeBioSource( BioSource bioSource, boolean synchronizeAnnotatedAttributes ) { bioSource.setCvCellType( synchronize( bioSource.getCvCellType() ) ); bioSource.setCvTissue( synchronize( bioSource.getCvTissue() ) ); if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( bioSource ); } }
public BioSource cloneBioSource(BioSource bioSource) throws IntactClonerException { if (bioSource == null) return null; BioSource clone = new BioSource(); clonerManager.addClone(bioSource, clone); clone.setTaxId(bioSource.getTaxId()); clone.setCvCellType(clone(bioSource.getCvCellType())); clone.setCvTissue(clone(bioSource.getCvTissue())); return clone; }
public BioSource cloneBioSource(BioSource bioSource) throws IntactClonerException { if (bioSource == null) return null; BioSource clone = new BioSource(); clonerManager.addClone(bioSource, clone); clone.setTaxId(bioSource.getTaxId()); clone.setCvCellType(clone(bioSource.getCvCellType())); clone.setCvTissue(clone(bioSource.getCvTissue())); return clone; }
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; }
bs.setCvTissue( bsTissue ); needUpdate = true;
bs.setCvTissue( bsTissue ); needUpdate = true;
bs.setCvTissue( bsTissue ); needUpdate = true;