- JSONObject val = (JSONObject) jp.parse(br);
- String type = val.get(OBJECT_TYPE).toString();
- if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
- {
- geneId = val.get(ID).toString();
- }
- else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
- {
- geneId = val.get(PARENT).toString();
- }
- else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
- {
- String transcriptId = val.get(PARENT).toString();
- try
- {
- geneId = getGeneId(transcriptId);
- } catch (StackOverflowError e)
- {
- /*
- * unlikely data condition error!
- */
- System.err
- .println("** Ensembl lookup "
- + getUrl(transcriptId).toString()
- + " looping on Parent!");
- }
- }
- } catch (ParseException | IOException e)
+ final String species = json.get("species").toString();
+ final String assembly = json.get("assembly_name").toString();
+ final String chromosome = json.get("seq_region_name").toString();
+ String strand = json.get("strand").toString();
+ int start = Integer.parseInt(json.get("start").toString());
+ int end = Integer.parseInt(json.get("end").toString());
+ int fromEnd = end - start + 1;
+ boolean reverseStrand = "-1".equals(strand);
+ int toStart = reverseStrand ? end : start;
+ int toEnd = reverseStrand ? start : end;
+ List<int[]> fromRange = Collections
+ .singletonList(new int[]
+ { 1, fromEnd });
+ List<int[]> toRange = Collections
+ .singletonList(new int[]
+ { toStart, toEnd });
+ final Mapping map = new Mapping(
+ new MapList(fromRange, toRange, 1, 1));
+ return new GeneLocus(species == null ? "" : species, assembly,
+ chromosome, map);
+ } catch (NullPointerException | NumberFormatException e)