X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSymbol.java;h=0d7986466334b6c96e067713d8a7f1983e02eed5;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=1c47f11ff81a0b9b5361384ad3b3fcf9ed4234af;hpb=a61896507a80dd6dcafaee02a872678022afe943;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 1c47f11..0d79864 100644
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.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 java.io.BufferedReader;
@@ -25,11 +45,13 @@ public class EnsemblSymbol extends EnsemblXref
/**
* Constructor given the target domain to fetch data from
*
- * @param d
+ * @param domain
+ * @param dbName
+ * @param dbVersion
*/
- public EnsemblSymbol(String d)
+ public EnsemblSymbol(String domain, String dbName, String dbVersion)
{
- super(d);
+ super(domain, dbName, dbVersion);
}
/**
@@ -69,8 +91,7 @@ public class EnsemblSymbol extends EnsemblXref
protected URL getUrl(String id, Species species)
{
String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
- + id
- + "?content-type=application/json";
+ + id + "?content-type=application/json";
try
{
return new URL(url);
@@ -92,7 +113,7 @@ public class EnsemblSymbol extends EnsemblXref
List result = new ArrayList();
List ids = new ArrayList();
ids.add(identifier);
-
+
String[] queries = identifier.split(getAccessionSeparator());
BufferedReader br = null;
try