import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.util.DBRefUtils;
+import jalview.util.JSONUtils;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
* an Ensembl stable identifier
* @return
*/
+ @SuppressWarnings("unchecked")
public List<DBRefEntry> getCrossReferences(String identifier)
{
List<DBRefEntry> result = new ArrayList<>();
List<String> ids = new ArrayList<>();
ids.add(identifier);
- BufferedReader br = null;
try
{
- URL url = getUrl(identifier);
- if (url != null)
- {
- br = getHttpResponse(url, ids);
- if (br != null)
- {
- result = parseResponse(br);
- }
- }
- } catch (IOException e)
- {
- // ignore
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
-
- return result;
- }
-
- /**
- * Parses "primary_id" and "dbname" values from the JSON response and
- * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
- * don't parse "synonyms" as they appear to be either redirected or obsolete
- * in Uniprot.
- *
- * @param br
- * @return
- * @throws IOException
- */
- protected List<DBRefEntry> parseResponse(BufferedReader br)
- throws IOException
- {
- JSONParser jp = new JSONParser();
- List<DBRefEntry> result = new ArrayList<>();
- try
- {
- JSONArray responses = (JSONArray) jp.parse(br);
- Iterator rvals = responses.iterator();
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(identifier), ids, -1, MODE_ITERATOR, null);
while (rvals.hasNext())
{
- JSONObject val = (JSONObject) rvals.next();
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
String db = val.get("dbname").toString();
String id = val.get("primary_id").toString();
if (db != null && id != null
result.add(dbref);
}
}
- } catch (ParseException e)
+ } catch (ParseException | IOException e)
{
// ignore
}
return result;
}
+// /**
+// * Parses "primary_id" and "dbname" values from the JSON response and
+// * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
+// * don't parse "synonyms" as they appear to be either redirected or obsolete
+// * in Uniprot.
+// *
+// * @param br
+// * @return
+// * @throws IOException
+// */
+// @SuppressWarnings("unchecked")
+//protected List<DBRefEntry> parseResponse(BufferedReader br)
+// throws IOException
+// {
+// return result;
+// }
+//
private String xrefVersion = "ENSEMBL:0";
/**