2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.ensembl;
23 import jalview.bin.Cache;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.GeneLociI;
26 import jalview.util.MapList;
28 import java.io.BufferedReader;
29 import java.io.IOException;
30 import java.net.MalformedURLException;
32 import java.util.Arrays;
33 import java.util.Collections;
34 import java.util.List;
36 import org.json.simple.JSONObject;
37 import org.json.simple.parser.JSONParser;
38 import org.json.simple.parser.ParseException;
41 * A client for the Ensembl /lookup REST endpoint, used to find the gene
42 * identifier given a gene, transcript or protein identifier, or to extract the
43 * species or chromosomal coordinates from the same service response
47 public class EnsemblLookup extends EnsemblRestClient
49 private static final String SPECIES = "species";
52 * Default constructor (to use rest.ensembl.org)
54 public EnsemblLookup()
60 * Constructor given the target domain to fetch data from
64 public EnsemblLookup(String d)
70 public String getDbName()
76 public AlignmentI getSequenceRecords(String queries) throws Exception
82 protected URL getUrl(List<String> ids) throws MalformedURLException
84 String identifier = ids.get(0);
85 return getUrl(identifier, null);
89 * Gets the url for lookup of the given identifier, optionally with objectType
90 * also specified in the request
96 protected URL getUrl(String identifier, String objectType)
98 String url = getDomain() + "/lookup/id/" + identifier
100 if (objectType != null)
102 url += "&" + OBJECT_TYPE + "=" + objectType;
108 } catch (MalformedURLException e)
115 protected boolean useGetRequest()
121 protected String getRequestMimeType(boolean multipleIds)
123 return "application/json";
127 protected String getResponseMimeType()
129 return "application/json";
133 * Returns the gene id related to the given identifier (which may be for a
134 * gene, transcript or protein)
139 public String getGeneId(String identifier)
141 return parseGeneId(getResult(identifier, null));
145 * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
146 * given identifier, or null if not found
151 public String getSpecies(String identifier)
153 String species = null;
154 JSONObject json = getResult(identifier, null);
157 Object o = json.get(SPECIES);
160 species = o.toString();
167 * Calls the /lookup/id rest service and returns the response as a JSONObject,
168 * or null if any error
175 protected JSONObject getResult(String identifier, String objectType)
177 List<String> ids = Arrays.asList(new String[] { identifier });
179 BufferedReader br = null;
182 URL url = getUrl(identifier, objectType);
185 br = getHttpResponse(url, ids);
187 return br == null ? null : (JSONObject) (new JSONParser().parse(br));
188 } catch (IOException | ParseException e)
190 System.err.println("Error parsing " + identifier + " lookup response "
200 } catch (IOException e)
209 * Parses the JSON response and returns the gene identifier, or null if not
210 * found. If the returned object_type is Gene, returns the id, if Transcript
211 * returns the Parent. If it is Translation (peptide identifier), then the
212 * Parent is the transcript identifier, so we redo the search with this value,
213 * specifying that object_type should be Transcript.
218 protected String parseGeneId(JSONObject json)
222 // e.g. lookup failed with 404 not found
226 String geneId = null;
227 String type = json.get(OBJECT_TYPE).toString();
228 if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
230 // got the gene - just returns its id
231 geneId = json.get(JSON_ID).toString();
233 else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
235 // got the transcript - return its (Gene) Parent
236 geneId = json.get(PARENT).toString();
238 else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
240 // got the protein - look up its Parent, restricted to type Transcript
241 String transcriptId = json.get(PARENT).toString();
242 geneId = parseGeneId(getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT));
249 * Calls the /lookup/id rest service for the given id, and if successful,
250 * parses and returns the gene's chromosomal coordinates
255 public GeneLociI getGeneLoci(String geneId)
257 return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE));
261 * Parses the /lookup/id response for species, asssembly_name,
262 * seq_region_name, start, end and returns an object that wraps them, or null
268 GeneLociI parseGeneLoci(JSONObject json)
277 final String species = json.get("species").toString();
278 final String assembly = json.get("assembly_name").toString();
279 final String chromosome = json.get("seq_region_name").toString();
280 String strand = json.get("strand").toString();
281 int start = Integer.parseInt(json.get("start").toString());
282 int end = Integer.parseInt(json.get("end").toString());
283 int fromEnd = end - start + 1;
284 boolean reverseStrand = "-1".equals(strand);
285 int toStart = reverseStrand ? end : start;
286 int toEnd = reverseStrand ? start : end;
287 List<int[]> fromRange = Collections.singletonList(new int[] { 1,
289 List<int[]> toRange = Collections.singletonList(new int[] { toStart,
291 final MapList map = new MapList(fromRange, toRange, 1, 1);
292 return new GeneLociI()
296 public String getSpeciesId()
298 return species == null ? "" : species;
302 public String getAssemblyId()
308 public String getChromosomeId()
314 public MapList getMap()
319 } catch (NullPointerException | NumberFormatException e)
321 Cache.log.error("Error looking up gene loci: " + e.getMessage());