/** * Returns a <code>List<String></code> of distinct gene ids suitable for autocomplete * sourcing. * * @return a <code>List<String></code> of gene ids suitable for autocomplete sourcing. */ public List<String> getGeneIds() { List<GenesDAO> genesDAOList = getGenes(); List<String> targetList = new ArrayList(); if (genesDAOList != null) { for (GenesDAO genesDAO : genesDAOList) { String sId_gene = Integer.toString(genesDAO.getId_gene()); targetList.add(Utils.wrap(sId_gene, "\"")); } } logger.debug("targetList count = " + targetList.size()); return targetList; }
/** * Transforms a <code>List<GenesDAO></code> to a JSON string. * * @param genesDAOList the list to be transformed * @return the transformed JSON string */ public static String toJSON(List<GenesDAO> genesDAOList) { JSONArray jsonList = new JSONArray(); for (GenesDAO gene : genesDAOList) { JSONObject jsonGeneDAO = new JSONObject(); jsonGeneDAO.put("centimorgan", gene.getCentimorgan() == null ? "" : gene.getCentimorgan()); jsonGeneDAO.put("chromosome", gene.getChromosome() == null ? "" : gene.getChromosome()); jsonGeneDAO.put("cytoband", gene.getCytoband() == null ? "" : gene.getCytoband()); jsonGeneDAO.put("ensembl_ref", gene.getEnsembl_ref() == null ? "" : gene.getEnsembl_ref()); jsonGeneDAO.put( "founder_line_number", gene.getFounder_line_number() == null ? "" : gene.getFounder_line_number()); jsonGeneDAO.put("id_gene", Integer.toString(gene.getId_gene())); jsonGeneDAO.put("mgi_ref", gene.getMgi_ref() == null ? "" : gene.getMgi_ref()); jsonGeneDAO.put("name", gene.getName() == null ? "" : gene.getName()); jsonGeneDAO.put( "plasmid_construct", gene.getPlasmid_construct() == null ? "" : gene.getPlasmid_construct()); jsonGeneDAO.put("promoter", gene.getPromoter() == null ? "" : gene.getPromoter()); jsonGeneDAO.put("species", gene.getSpecies() == null ? "" : gene.getSpecies()); jsonGeneDAO.put("symbol", gene.getSymbol() == null ? "" : gene.getSymbol()); if ((gene.getSynonyms() != null) && (gene.getSynonyms().size() > 0)) { JSONArray synonyms = new JSONArray(); Iterator<Syn_GenesDAO> iterator = gene.getSynonyms().iterator(); while (iterator.hasNext()) { Syn_GenesDAO syn_genesDAO = iterator.next(); JSONObject synonym = new JSONObject(); synonym.put("id_syn", Integer.toString(syn_genesDAO.getId_syn())); synonym.put("name", syn_genesDAO.getName()); synonym.put("symbol", syn_genesDAO.getSymbol()); synonyms.add(synonym); } jsonGeneDAO.put("synonyms", synonyms); } jsonList.add(jsonGeneDAO); } // Gson dosn't reserve space for fields with null values!!!! //////// Gson gson = new Gson(); //////// String s = gson.toJson(genesDAOList); //////// System.out.println(s); //////// return s; return jsonList.toString(); }