X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=eb8f90ee738dcb1391137e6d0e755284df00bdf4;hb=defcce0ef74ffc0923b4387bcb5f0d867bf64831;hp=cd792b571808cab16602c7f656c80ccdd88b355d;hpb=550c391f0c113658e540783dc89034a34280ef18;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index cd792b5..eb8f90e 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.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;
@@ -13,9 +33,34 @@ import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+/**
+ * A client for the Ensembl lookup REST endpoint; used to find the Parent gene
+ * identifier given a transcript identifier.
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblLookup extends EnsemblRestClient
{
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
+ public EnsemblLookup()
+ {
+ super();
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param
+ */
+ public EnsemblLookup(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
@@ -41,7 +86,7 @@ public class EnsemblLookup extends EnsemblRestClient
*/
protected URL getUrl(String identifier)
{
- String url = ENSEMBL_REST + "/lookup/id/" + identifier
+ String url = getDomain() + "/lookup/id/" + identifier
+ "?content-type=application/json";
try
{
@@ -80,7 +125,7 @@ public class EnsemblLookup extends EnsemblRestClient
public String getParent(String identifier)
{
List ids = Arrays.asList(new String[] { identifier });
-
+
BufferedReader br = null;
try
{