/**
* 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();
}
