*/
public class EnsemblSymbol extends EnsemblXref
{
+ private static final String GENE = "gene";
+ private static final String TYPE = "type";
/**
* Constructor given the target domain to fetch data from
*
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String id = val.get("id").toString();
- String type = val.get("type").toString();
- if (id != null && "gene".equals(type))
+ String id = val.get(JSON_ID).toString();
+ String type = val.get(TYPE).toString();
+ if (id != null && GENE.equals(type))
{
result = id;
break;
StringBuilder sb = new StringBuilder();
sb.append(getDomain()).append("/xrefs/symbol/")
.append(species.toString()).append("/").append(id)
- .append("?content-type=application/json");
+ .append(CONTENT_TYPE_JSON);
for (String t : type)
{
sb.append("&object_type=").append(t);
{
for (String query : queries)
{
- for (Species taxon : Species.values())
+ for (Species taxon : Species.getModelOrganisms())
{
- if (taxon.isModelOrganism())
+ URL url = getUrl(query, taxon, GENE);
+ if (url != null)
{
- URL url = getUrl(query, taxon, "gene");
- if (url != null)
+ br = getHttpResponse(url, ids);
+ if (br != null)
{
- br = getHttpResponse(url, ids);
- if (br != null)
+ String geneId = parseSymbolResponse(br);
+ if (geneId != null && !result.contains(geneId))
{
- String geneId = parseSymbolResponse(br);
- if (geneId != null && !result.contains(geneId))
- {
- result.add(geneId);
- }
+ result.add(geneId);
}
}
}