/** * Creates a new {@link SpeciesReferenceFilter} that only accepts instances of * {@link SpeciesReference} pointing to the id of the given {@link Species}. * * @param species * the {@link Species} of interest. */ public SpeciesReferenceFilter(Species species) { this(species.getId(), species.getName()); setFilterForSpecies(true); }
private void processSpecies(ListOf<Species> list) { // process all species for (Species s : list) { String id = s.getId(); ONDEXConcept concept = null; // treat enzymes differently if (id.startsWith("enz_")) { concept = graph.getFactory().createConcept(id, dataSourceBrenda, ccEnzyme, evidence); // EC number is an ambiguous accession for an enzyme String ec = id.substring(7); ec = ec.replaceAll("_", "."); concept.createConceptAccession(ec, dataSourceEC, true); } else { concept = graph.getFactory().createConcept(id, dataSourceBrenda, ccComp, evidence); } // add preferred concept name String name = s.getName(); concept.createConceptName(name, true); concepts.put(id, concept); } }
for (String potentialYName : species.getName().split(":")) { if (potentialYName.matches("Y\\w{2}\\d{3}\\w{1,2}(\\-\\w)?")) { speciesC.createConceptAccession(potentialYName, dataSourceMips, false);
for (String potentialYName : species.getName().split(":")) { if (potentialYName.matches("Y\\w{2}\\d{3}\\w{1,2}(\\-\\w)?")) { speciesC.createConceptAccession(potentialYName, dataSourceMips, false);