JAL-2189 apply license

[jalview.git] / src / jalview / ext / ensembl / EnsemblSymbol.java

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 08f26c7..0d79864 100644 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * 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);
   }
 
   /**
@@ -40,7 +62,7 @@ public class EnsemblSymbol extends EnsemblXref
    * @return
    * @throws IOException
    */
-  protected String parseResponse(BufferedReader br)
+  protected String parseSymbolResponse(BufferedReader br)
           throws IOException
   {
     JSONParser jp = new JSONParser();
@@ -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<String> result = new ArrayList<String>();
     List<String> ids = new ArrayList<String>();
     ids.add(identifier);
-  
+
     String[] queries = identifier.split(getAccessionSeparator());
     BufferedReader br = null;
     try
@@ -108,7 +129,7 @@ public class EnsemblSymbol extends EnsemblXref
             {
               br = getHttpResponse(url, ids);
             }
-            String geneId = parseResponse(br);
+            String geneId = parseSymbolResponse(br);
             if (geneId != null)
             {
               result.add(geneId);