X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblXref.java;h=c0b00b182f8fc528974dff004831e33607c82f4d;hb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;hp=6a4f369def30e72345fc5fe2a77e86ec7fedfeb0;hpb=a9f0472fe6fd4737b47d7955d198e76923e6aabc;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index 6a4f369..c0b00b1 100644
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -1,3 +1,23 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
import jalview.datamodel.AlignmentI;
@@ -17,13 +37,37 @@ import org.json.simple.JSONObject;
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
@@ -35,8 +79,7 @@ public class EnsemblXref extends EnsemblRestClient
@Override
protected URL getUrl(List ids) throws MalformedURLException
{
- // TODO Auto-generated method stub
- return null;
+ return getUrl(ids.get(0));
}
@Override
@@ -60,15 +103,15 @@ public class EnsemblXref extends EnsemblRestClient
/**
* 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 getCrossReferences(String identifier,
- String... database)
+ public List getCrossReferences(String identifier)
{
List result = new ArrayList();
List ids = new ArrayList();
@@ -77,22 +120,12 @@ public class EnsemblXref extends EnsemblRestClient
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);
- }
- for (DBRefEntry xref : parseResponse(br))
- {
- if (!result.contains(xref))
- {
- result.add(xref);
- }
- }
- br.close();
+ br = getHttpResponse(url, ids);
}
+ return (parseResponse(br));
} catch (IOException e)
{
// ignore
@@ -114,8 +147,10 @@ public class EnsemblXref extends EnsemblRestClient
}
/**
- * 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
@@ -134,11 +169,15 @@ public class EnsemblXref extends EnsemblRestClient
{
JSONObject val = (JSONObject) rvals.next();
String dbName = val.get("dbname").toString();
+ if (dbName.equals(GO_GENE_ONTOLOGY))
+ {
+ continue;
+ }
String id = val.get("primary_id").toString();
if (dbName != null && id != null)
{
dbName = DBRefUtils.getCanonicalName(dbName);
- DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
+ DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
result.add(dbref);
}
}
@@ -149,10 +188,30 @@ public class EnsemblXref extends EnsemblRestClient
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);