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
45 private static final String SPECIES = "species";
47 private static final String PARENT = "Parent";
50 * Default constructor (to use rest.ensembl.org)
52 public EnsemblLookup()
58 * Constructor given the target domain to fetch data from
62 public EnsemblLookup(String d)
68 public String getDbName()
74 public AlignmentI getSequenceRecords(String queries) throws Exception
80 protected URL getUrl(List<String> ids) throws MalformedURLException
82 String identifier = ids.get(0);
83 return getUrl(identifier);
90 protected URL getUrl(String identifier)
92 String url = getDomain() + "/lookup/id/" + identifier
93 + "?content-type=application/json";
97 } catch (MalformedURLException e)
104 protected boolean useGetRequest()
110 protected String getRequestMimeType(boolean multipleIds)
112 return "application/json";
116 protected String getResponseMimeType()
118 return "application/json";
122 * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
123 * given identifier, or null if not found
128 public String getParent(String identifier)
130 return getAttribute(identifier, PARENT);
134 * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
135 * given identifier, or null if not found
140 public String getSpecies(String identifier)
142 return getAttribute(identifier, SPECIES);
150 protected String getAttribute(String identifier, String attribute)
152 List<String> ids = Arrays.asList(new String[] { identifier });
154 BufferedReader br = null;
157 URL url = getUrl(identifier);
160 br = getHttpResponse(url, ids);
162 return (parseResponse(br, attribute));
163 } catch (IOException e)
174 } catch (IOException e)
183 * Parses the value of 'attribute' from the JSON response and returns the
184 * value, or null if not found
189 * @throws IOException
191 protected String parseResponse(BufferedReader br, String attribute) throws IOException
193 String parent = null;
194 JSONParser jp = new JSONParser();
197 JSONObject val = (JSONObject) jp.parse(br);
198 parent = val.get(attribute).toString();
199 } catch (ParseException | NullPointerException e)