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 java.io.IOException;
24 import java.net.MalformedURLException;
26 import java.util.ArrayList;
27 import java.util.Iterator;
28 import java.util.List;
31 import org.json.simple.parser.ParseException;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.util.DBRefUtils;
38 * A class to fetch cross-references from Ensembl by calling the /xrefs REST
42 * @see http://rest.ensembl.org/documentation/info/xref_id
44 class EnsemblXref extends EnsemblRestClient
47 private static final String GO_GENE_ONTOLOGY = "GO";
49 private String dbName = "ENSEMBL (xref)";
52 * Constructor given the target domain to fetch data from
56 public EnsemblXref(String d, String dbSource, String version)
60 xrefVersion = dbSource + ":" + version;
65 public String getDbName()
71 public AlignmentI getSequenceRecords(String queries) throws Exception
77 protected URL getUrl(List<String> ids) throws MalformedURLException
79 return getUrl(ids.get(0));
83 protected boolean useGetRequest()
89 * Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
90 * ("primary_id") for the given identifier (Ensembl accession id) and database
91 * names. The "dbname" returned by Ensembl is canonicalised to Jalview's
92 * standard version, and a DBRefEntry constructed. Currently takes all
93 * identifiers apart from GO terms and synonyms.
96 * an Ensembl stable identifier
99 @SuppressWarnings("unchecked")
100 public List<DBRefEntry> getCrossReferences(String identifier)
102 List<DBRefEntry> result = new ArrayList<>();
103 List<String> ids = new ArrayList<>();
108 Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(identifier), ids, -1, MODE_ITERATOR, null);
109 while (rvals.hasNext())
111 Map<String, Object> val = (Map<String, Object>) rvals.next();
112 String db = val.get("dbname").toString();
113 String id = val.get("primary_id").toString();
114 if (db != null && id != null
115 && !GO_GENE_ONTOLOGY.equals(db))
117 db = DBRefUtils.getCanonicalName(db);
118 DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
122 } catch (ParseException | IOException e)
130 // * Parses "primary_id" and "dbname" values from the JSON response and
131 // * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
132 // * don't parse "synonyms" as they appear to be either redirected or obsolete
137 // * @throws IOException
139 // @SuppressWarnings("unchecked")
140 //protected List<DBRefEntry> parseResponse(BufferedReader br)
141 // throws IOException
146 private String xrefVersion = "ENSEMBL:0";
149 * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
153 public String getXRefVersion()
159 * Returns the URL for the REST endpoint to fetch all cross-references for an
160 * identifier. Note this may return protein cross-references for nucleotide.
161 * Filter the returned list as required.
166 protected URL getUrl(String identifier)
168 String url = getDomain() + "/xrefs/id/" + identifier
169 + CONTENT_TYPE_JSON + "&all_levels=1";
173 } catch (MalformedURLException e)