X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblXref.java;h=77768a6fa94243a7b354545010333b6547370e36;hb=f59dd9efbb3dfc313ab0b0507832e21cd0076fe1;hp=313572f0639e01419292a35d3464dd232958cb55;hpb=76de4fc452184b56e01960d05cb2235b1807e836;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index 313572f..77768a6 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;
@@ -41,7 +61,7 @@ class EnsemblXref extends EnsemblRestClient
super(d);
dbName = dbSource;
xrefVersion = dbSource + ":" + version;
-
+
}
@Override
@@ -68,18 +88,6 @@ class EnsemblXref extends EnsemblRestClient
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
* ("primary_id") for the given identifier (Ensembl accession id) and database
@@ -93,8 +101,8 @@ class EnsemblXref extends EnsemblRestClient
*/
public List getCrossReferences(String identifier)
{
- List result = new ArrayList();
- List ids = new ArrayList();
+ List result = new ArrayList<>();
+ List ids = new ArrayList<>();
ids.add(identifier);
BufferedReader br = null;
@@ -104,8 +112,11 @@ class EnsemblXref extends EnsemblRestClient
if (url != null)
{
br = getHttpResponse(url, ids);
+ if (br != null)
+ {
+ result = parseResponse(br);
+ }
}
- return (parseResponse(br));
} catch (IOException e)
{
// ignore
@@ -140,7 +151,7 @@ class EnsemblXref extends EnsemblRestClient
throws IOException
{
JSONParser jp = new JSONParser();
- List result = new ArrayList();
+ List result = new ArrayList<>();
try
{
JSONArray responses = (JSONArray) jp.parse(br);
@@ -148,16 +159,13 @@ class EnsemblXref extends EnsemblRestClient
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String dbName = val.get("dbname").toString();
- if (dbName.equals(GO_GENE_ONTOLOGY))
- {
- continue;
- }
+ String db = val.get("dbname").toString();
String id = val.get("primary_id").toString();
- if (dbName != null && id != null)
+ if (db != null && id != null
+ && !GO_GENE_ONTOLOGY.equals(db))
{
- dbName = DBRefUtils.getCanonicalName(dbName);
- DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
result.add(dbref);
}
}
@@ -191,7 +199,7 @@ class EnsemblXref extends EnsemblRestClient
protected URL getUrl(String identifier)
{
String url = getDomain() + "/xrefs/id/" + identifier
- + "?content-type=application/json&all_levels=1";
+ + CONTENT_TYPE_JSON + "&all_levels=1";
try
{
return new URL(url);