JAL-2105 REST versions updated to 6.1 (Ensembl) 6.0 (Ensemblgenomes)

[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..671bfec 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);
   }
 
   /**
@@ -40,8 +62,7 @@ public class EnsemblSymbol extends EnsemblXref
    * @return
    * @throws IOException
    */
-  protected String parseResponse(BufferedReader br)
-          throws IOException
+  protected String parseSymbolResponse(BufferedReader br) throws IOException
   {
     JSONParser jp = new JSONParser();
     String result = null;
@@ -53,7 +74,8 @@ public class EnsemblSymbol extends EnsemblXref
       {
         JSONObject val = (JSONObject) rvals.next();
         String id = val.get("id").toString();
-        if (id != null && isGeneIdentifier(id))
+        String type = val.get("type").toString();
+        if (id != null && "gene".equals(type))
         {
           result = id;
           break;
@@ -66,13 +88,31 @@ public class EnsemblSymbol extends EnsemblXref
     return result;
   }
 
-  protected URL getUrl(String id, Species species)
+  /**
+   * Constructs the URL for the REST symbol endpoint
+   * 
+   * @param id
+   *          the accession id (Ensembl or external)
+   * @param species
+   *          a species name recognisable by Ensembl
+   * @param type
+   *          an optional type to filter the response (gene, transcript,
+   *          translation)
+   * @return
+   */
+  protected URL getUrl(String id, Species species, String... type)
   {
-    String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
-            + id
-            + "?content-type=application/json";
+    StringBuilder sb = new StringBuilder();
+    sb.append(getDomain()).append("/xrefs/symbol/")
+            .append(species.toString()).append("/").append(id)
+            .append("?content-type=application/json");
+    for (String t : type)
+    {
+      sb.append("&object_type=").append(t);
+    }
     try
     {
+      String url = sb.toString();
       return new URL(url);
     } catch (MalformedURLException e)
     {
@@ -87,12 +127,12 @@ public class EnsemblSymbol extends EnsemblXref
    * @param identifier
    * @return
    */
-  public List<String> getIds(String identifier)
+  public List<String> getGeneIds(String identifier)
   {
     List<String> result = new ArrayList<String>();
     List<String> ids = new ArrayList<String>();
     ids.add(identifier);
-  
+
     String[] queries = identifier.split(getAccessionSeparator());
     BufferedReader br = null;
     try
@@ -103,15 +143,18 @@ public class EnsemblSymbol extends EnsemblXref
         {
           if (taxon.isModelOrganism())
           {
-            URL url = getUrl(query, taxon);
+            URL url = getUrl(query, taxon, "gene");
             if (url != null)
             {
               br = getHttpResponse(url, ids);
-            }
-            String geneId = parseResponse(br);
-            if (geneId != null)
-            {
-              result.add(geneId);
+              if (br != null)
+              {
+                String geneId = parseSymbolResponse(br);
+                if (geneId != null && !result.contains(geneId))
+                {
+                  result.add(geneId);
+                }
+              }
             }
           }
         }