+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
import jalview.datamodel.AlignmentI;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
-public class EnsemblXref extends EnsemblRestClient
+/**
+ * A class to fetch cross-references from Ensembl by calling the /xrefs REST
+ * service
+ *
+ * @author gmcarstairs
+ * @see http://rest.ensembl.org/documentation/info/xref_id
+ */
+class EnsemblXref extends EnsemblRestClient
{
+ private static final String GO_GENE_ONTOLOGY = "GO";
+
+ private String dbName = "ENSEMBL (xref)";
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblXref(String d, String dbSource, String version)
+ {
+ super(d);
+ dbName = dbSource;
+ xrefVersion = dbSource + ":" + version;
+
+ }
+
@Override
public String getDbName()
{
- return "ENSEMBL (xref)";
+ return dbName;
}
@Override
@Override
protected URL getUrl(List<String> ids) throws MalformedURLException
{
- // TODO Auto-generated method stub
- return null;
+ return getUrl(ids.get(0));
}
@Override
/**
* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
* ("primary_id") for the given identifier (Ensembl accession id) and database
- * name. The "dbname" returned by Ensembl is canonicalised to Jalview's
- * standard version, and a DBRefEntry constructed.
+ * names. The "dbname" returned by Ensembl is canonicalised to Jalview's
+ * standard version, and a DBRefEntry constructed. Currently takes all
+ * identifiers apart from GO terms and synonyms.
*
* @param identifier
- * @param database
+ * an Ensembl stable identifier
* @return
*/
- public List<DBRefEntry> getCrossReferences(String identifier,
- String... database)
+ public List<DBRefEntry> getCrossReferences(String identifier)
{
List<DBRefEntry> result = new ArrayList<DBRefEntry>();
List<String> ids = new ArrayList<String>();
BufferedReader br = null;
try
{
- for (String db : database)
+ URL url = getUrl(identifier);
+ if (url != null)
{
- URL url = getUrl(identifier, db);
- if (url != null)
+ br = getHttpResponse(url, ids);
+ if (br != null)
{
- br = getHttpResponse(url, ids);
+ result = parseResponse(br);
}
- for (DBRefEntry xref : parseResponse(br))
- {
- if (!result.contains(xref))
- {
- result.add(xref);
- }
- }
- br.close();
}
} catch (IOException e)
{
}
/**
- * Parses "primary_id" and "dbname" values from the JSON response and returns
- * a list of DBRefEntry constructed.
+ * Parses "primary_id" and "dbname" values from the JSON response and
+ * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
+ * don't parse "synonyms" as they appear to be either redirected or obsolete
+ * in Uniprot.
*
* @param br
* @return
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String dbName = val.get("dbname").toString();
+ String dbname = val.get("dbname").toString();
+ if (GO_GENE_ONTOLOGY.equals(dbname))
+ {
+ continue;
+ }
String id = val.get("primary_id").toString();
- if (dbName != null && id != null)
+ if (dbname != null && id != null)
{
- dbName = DBRefUtils.getCanonicalName(dbName);
- DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
+ dbname = DBRefUtils.getCanonicalName(dbname);
+ DBRefEntry dbref = new DBRefEntry(dbname, getXRefVersion(), id);
result.add(dbref);
}
}
return result;
}
- protected URL getUrl(String identifier, String db)
+ private String xrefVersion = "ENSEMBL:0";
+
+ /**
+ * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
+ *
+ * @return
+ */
+ public String getXRefVersion()
+ {
+ return xrefVersion;
+ }
+
+ /**
+ * Returns the URL for the REST endpoint to fetch all cross-references for an
+ * identifier. Note this may return protein cross-references for nucleotide.
+ * Filter the returned list as required.
+ *
+ * @param identifier
+ * @return
+ */
+ protected URL getUrl(String identifier)
{
- String url = ENSEMBL_REST + "/xrefs/id/" + identifier
- + "?content-type=application/json&external_db=" + db;
+ String url = getDomain() + "/xrefs/id/" + identifier
+ + "?content-type=application/json&all_levels=1";
try
{
return new URL(url);
git://source.jalview.org / jalview.git / blobdiff