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
*
super(domain, dbName, dbVersion);
}
-// /**
-// * Returns the first "id" value in gene identifier format from the JSON
-// * response, or null if none found
-// *
-// * @param br
-// * @return
-// * @throws IOException
-// */
-// @SuppressWarnings("unchecked")
-//protected String parseSymbolResponse(BufferedReader br) throws IOException
-// {
-// }
+ // /**
+ // * Returns the first "id" value in gene identifier format from the JSON
+ // * response, or null if none found
+ // *
+ // * @param br
+ // * @return
+ // * @throws IOException
+ // */
+ // @SuppressWarnings("unchecked")
+ // protected String parseSymbolResponse(BufferedReader br) throws IOException
+ // {
+ // }
/**
* Constructs the URL for the REST symbol endpoint
{
for (Species taxon : Species.getModelOrganisms())
{
- String geneId = null;///parseSymbolResponse(br);
+ String geneId = null;/// parseSymbolResponse(br);
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(
+ getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR,
+ null);
if (rvals == null)
- continue;
+ continue;
while (rvals.hasNext())
{
Map<String, Object> val = (Map<String, Object>) rvals.next();
{
// ignore
}
-
+
if (geneId != null && !result.contains(geneId))
{
result.add(geneId);