- JSONObject val = (JSONObject) jp.parse(br);
- String type = val.get(OBJECT_TYPE).toString();
- if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
- {
- // got the gene - just returns its id
- geneId = val.get(JSON_ID).toString();
- }
- else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
- {
- // got the transcript - return its (Gene) Parent
- geneId = val.get(PARENT).toString();
- }
- else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
- {
- // got the protein - get its Parent, restricted to type Transcript
- String transcriptId = val.get(PARENT).toString();
- geneId = (String) getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT,
- reader -> parseGeneId(reader));
- }
- } catch (ParseException | IOException e)
+ // got the gene - just returns its id
+ geneId = json.get(JSON_ID).toString();
+ }
+ else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+ {
+ // got the transcript - return its (Gene) Parent
+ geneId = json.get(PARENT).toString();
+ }
+ else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))