/**
* 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();
}
/**
* Remaps null fields to empty strings suitable for use in the client.
*
* @param genesDAO the instance to remap
* @return the same instance, with nulls remapped to empty strings.
*/
private GenesDAO remapNulls(GenesDAO genesDAO) {
// Re-map null fields to empty strings.
if (genesDAO != null) {
if (genesDAO.getCentimorgan() == null) genesDAO.setCentimorgan("");
if (genesDAO.getChromosome() == null) genesDAO.setChromosome("");
if (genesDAO.getCytoband() == null) genesDAO.setCytoband("");
if (genesDAO.getEnsembl_ref() == null) genesDAO.setEnsembl_ref("");
if (genesDAO.getFounder_line_number() == null) genesDAO.setFounder_line_number("");
if (genesDAO.getLast_change() == null) genesDAO.setLast_change("");
if (genesDAO.getMgi_ref() == null) genesDAO.setMgi_ref("");
if (genesDAO.getName() == null) genesDAO.setName("");
if (genesDAO.getPlasmid_construct() == null) genesDAO.setPlasmid_construct("");
if (genesDAO.getPromoter() == null) genesDAO.setPromoter("");
if (genesDAO.getSpecies() == null) genesDAO.setSpecies("");
if (genesDAO.getSymbol() == null) genesDAO.setSymbol("");
if (genesDAO.getUsername() == null) genesDAO.setUsername("");
}
return genesDAO;
}
