*/
public class EnsemblLookup extends EnsemblRestClient
{
+ private static final String SPECIES = "species";
+
/**
- * keep track of last identifier retrieved to break loops
- */
- private String lastId;
-
- /**
* Default constructor (to use rest.ensembl.org)
*/
public EnsemblLookup()
return geneId;
}
+ /**
+ * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
+ * given identifier, or null if not found
+ *
+ * @param identifier
+ * @return
+ */
+ public String getSpecies(String identifier)
+ {
+ String species = null;
+ JSONObject json = getResult(identifier, null);
+ if (json != null)
+ {
+ Object o = json.get(SPECIES);
+ if (o != null)
+ {
+ species = o.toString();
+ }
+ }
+ return species;
+ }
+
+ /**
+ * Calls the /lookup/id rest service and returns the response as a JSONObject,
+ * or null if any error
+ *
+ * @param identifier
+ * @param objectType
+ * (optional)
+ * @return
+ */
+ protected JSONObject getResult(String identifier, String objectType)
+ {
+ List<String> ids = Arrays.asList(new String[] { identifier });
+
+ BufferedReader br = null;
+ try
+ {
-
+ URL url = getUrl(identifier, objectType);
+
- if (identifier.equals(lastId))
- {
- System.err.println("** Ensembl lookup " + url.toString()
- + " looping on Parent!");
- return null;
- }
-
- lastId = identifier;
-
+ if (url != null)
+ {
+ br = getHttpResponse(url, ids);
+ }
+ return br == null ? null : (JSONObject) (new JSONParser().parse(br));
+ } catch (IOException | ParseException e)
+ {
+ System.err.println("Error parsing " + identifier + " lookup response "
+ + e.getMessage());
+ return null;
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ /**
- * Parses the JSON response and returns the gene identifier, or null if not
- * found. If the returned object_type is Gene, returns the id, if Transcript
- * returns the Parent. If it is Translation (peptide identifier), then the
- * Parent is the transcript identifier, so we redo the search with this value,
- * specifying that object_type should be Transcript.
- *
- * @param jsonObject
- * @return
- */
- protected String parseGeneId(JSONObject json)
- {
- if (json == null)
- {
- // e.g. lookup failed with 404 not found
- return null;
- }
-
- String geneId = null;
- String type = json.get(OBJECT_TYPE).toString();
- if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
- {
- // 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))
- {
- // got the protein - look up its Parent, restricted to type Transcript
- String transcriptId = json.get(PARENT).toString();
- geneId = parseGeneId(getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT));
- }
-
- return geneId;
- }
-
- /**
+ * Calls the /lookup/id rest service for the given id, and if successful,
+ * parses and returns the gene's chromosomal coordinates
+ *
+ * @param geneId
+ * @return
+ */
+ public GeneLociI getGeneLoci(String geneId)
+ {
+ return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE));
+ }
+
+ /**
+ * Parses the /lookup/id response for species, asssembly_name,
+ * seq_region_name, start, end and returns an object that wraps them, or null
+ * if unsuccessful
+ *
+ * @param json
+ * @return
+ */
+ GeneLociI parseGeneLoci(JSONObject json)
+ {
+ if (json == null)
+ {
+ return null;
+ }
+
+ try
+ {
+ 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 MapList map = new MapList(fromRange, toRange, 1, 1);
+ return new GeneLociI()
+ {
+
+ @Override
+ public String getSpeciesId()
+ {
+ return species == null ? "" : species;
+ }
+
+ @Override
+ public String getAssemblyId()
+ {
+ return assembly;
+ }
+
+ @Override
+ public String getChromosomeId()
+ {
+ return chromosome;
+ }
+
+ @Override
+ public MapList getMap()
+ {
+ return map;
+ }
+ };
+ } catch (NullPointerException | NumberFormatException e)
+ {
+ Cache.log.error("Error looking up gene loci: " + e.getMessage());
+ e.printStackTrace();
+ }
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff