public static Organism createOrganism(int taxid, String name) { Organism organism = new Organism(); organism.setNames(createNames(name, null)); organism.setNcbiTaxId(taxid); return organism; }
public Organism intactToPsi(BioSource intactObject) { intactStartConversation(intactObject); Organism organism = new Organism(); // populates names // Set id, annotations, xrefs and aliases PsiConverterUtils.populateNames(intactObject, organism, aliasConverter); // taxId if (intactObject.getTaxId() != null){ organism.setNcbiTaxId(Integer.valueOf(intactObject.getTaxId())); } else { log.error("BioSource without taxId : " + intactObject.getShortLabel()); } // cell type final CvCellType intactCellType = intactObject.getCvCellType(); if (intactCellType != null) { CellType psiCellType = cellTypeConverter.intactToPsi(intactCellType); organism.setCellType(psiCellType); } // tissue final CvTissue intactTissue = intactObject.getCvTissue(); if (intactTissue != null) { Tissue psiTissue = tissueConverter.intactToPsi(intactTissue); organism.setTissue(psiTissue); } intactEndConversion(intactObject); return organism; }
xmlOrganism = new Organism(); xmlOrganism.setNcbiTaxId(ncbiTaxId); xmlOrganism.setNames(names);
Organism organism = new Organism(); organism.setNcbiTaxId(hostOrganism.getNcbiTaxId()); organism.setNames(hostOrganism.getNames());
public psidev.psi.mi.xml.model.Organism fromJaxb( psidev.psi.mi.xml254.jaxb.BioSource jOrganism ) throws ConverterException { if ( jOrganism == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Organism." ); } psidev.psi.mi.xml.model.Organism mOrganism = new psidev.psi.mi.xml.model.Organism(); // Initialise the model reading the Jaxb object // 1. set attributes mOrganism.setNcbiTaxId( jOrganism.getNcbiTaxId() ); // 2. set encapsulated objects // names if ( jOrganism.getNames() != null ) { mOrganism.setNames( namesConverter.fromJaxb( jOrganism.getNames() ) ); } // cell type if ( jOrganism.getCellType() != null ) { mOrganism.setCellType( openCvTypeConverter.fromJaxb( jOrganism.getCellType(), CellType.class ) ); } // compartment if ( jOrganism.getCompartment() != null ) { mOrganism.setCompartment( openCvTypeConverter.fromJaxb( jOrganism.getCompartment(), Compartment.class ) ); } // tissue if ( jOrganism.getTissue() != null ) { mOrganism.setTissue( openCvTypeConverter.fromJaxb( jOrganism.getTissue(), Tissue.class ) ); } return mOrganism; }
public psidev.psi.mi.xml.model.Organism fromJaxb( psidev.psi.mi.xml253.jaxb.BioSourceType jOrganism ) throws ConverterException { if ( jOrganism == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Organism." ); } psidev.psi.mi.xml.model.Organism mOrganism = new psidev.psi.mi.xml.model.Organism(); // Initialise the model reading the Jaxb object // 1. set attributes mOrganism.setNcbiTaxId( jOrganism.getNcbiTaxId() ); // 2. set encapsulated objects // names if ( jOrganism.getNames() != null ) { mOrganism.setNames( namesConverter.fromJaxb( jOrganism.getNames() ) ); } // cell type if ( jOrganism.getCellType() != null ) { mOrganism.setCellType( openCvTypeConverter.fromJaxb( jOrganism.getCellType(), CellType.class ) ); } // compartment if ( jOrganism.getCompartment() != null ) { mOrganism.setCompartment( openCvTypeConverter.fromJaxb( jOrganism.getCompartment(), Compartment.class ) ); } // tissue if ( jOrganism.getTissue() != null ) { mOrganism.setTissue( openCvTypeConverter.fromJaxb( jOrganism.getTissue(), Tissue.class ) ); } return mOrganism; }
Organism organism = new Organism(); organism.setNcbiTaxId(hostOrganism.getNcbiTaxId()); organism.setNames(hostOrganism.getNames());
psidev.psi.mi.xml.model.Organism organism = new psidev.psi.mi.xml.model.Organism();