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.datamodel.AlignmentI;
25 import java.io.BufferedReader;
26 import java.io.IOException;
27 import java.net.MalformedURLException;
29 import java.util.Arrays;
30 import java.util.List;
32 import org.json.simple.JSONObject;
33 import org.json.simple.parser.JSONParser;
34 import org.json.simple.parser.ParseException;
37 * A client for the Ensembl lookup REST endpoint; used to find the Parent gene
38 * identifier given a transcript identifier.
43 public class EnsemblLookup extends EnsemblRestClient
46 private static final String OBJECT_TYPE_TRANSLATION = "Translation";
47 private static final String PARENT = "Parent";
48 private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
49 private static final String ID = "id";
50 private static final String OBJECT_TYPE_GENE = "Gene";
51 private static final String OBJECT_TYPE = "object_type";
54 * Default constructor (to use rest.ensembl.org)
56 public EnsemblLookup()
62 * Constructor given the target domain to fetch data from
66 public EnsemblLookup(String d)
72 public String getDbName()
78 public AlignmentI getSequenceRecords(String queries) throws Exception
84 protected URL getUrl(List<String> ids) throws MalformedURLException
86 String identifier = ids.get(0);
87 return getUrl(identifier);
94 protected URL getUrl(String identifier)
96 String url = getDomain() + "/lookup/id/" + identifier
101 } catch (MalformedURLException e)
108 protected boolean useGetRequest()
114 protected String getRequestMimeType(boolean multipleIds)
116 return "application/json";
120 protected String getResponseMimeType()
122 return "application/json";
126 * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
127 * given identifier, or null if not found
132 public String getGeneId(String identifier)
134 List<String> ids = Arrays.asList(new String[] { identifier });
136 BufferedReader br = null;
139 URL url = getUrl(identifier);
142 br = getHttpResponse(url, ids);
144 return br == null ? null : parseResponse(br);
145 } catch (IOException e)
156 } catch (IOException e)
165 * Parses the JSON response and returns the gene identifier, or null if not
166 * found. If the returned object_type is Gene, returns the id, if Transcript
167 * returns the Parent. If it is Translation (peptide identifier), then the
168 * Parent is the transcript identifier, so we redo the search with this value.
172 * @throws IOException
174 protected String parseResponse(BufferedReader br) throws IOException
176 String geneId = null;
177 JSONParser jp = new JSONParser();
180 JSONObject val = (JSONObject) jp.parse(br);
181 String type = val.get(OBJECT_TYPE).toString();
182 if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
184 geneId = val.get(ID).toString();
186 else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
188 geneId = val.get(PARENT).toString();
190 else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
192 String transcriptId = val.get(PARENT).toString();
195 geneId = getGeneId(transcriptId);
196 } catch (StackOverflowError e)
199 * unlikely data condition error!
202 .println("** Ensembl lookup "
203 + getUrl(transcriptId).toString()
204 + " looping on Parent!");
207 } catch (ParseException e)