X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=31da9c005bbcc0b5cf151ba30b39d142098a49b5;hb=ccbd3e0bfd34533d8e98b7ef9a6cb48d9684b3da;hp=c5945aea124abf085fa84a0e23b66d84004c3892;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index c5945ae..31da9c0 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
@@ -23,6 +43,13 @@ import org.json.simple.parser.ParseException;
 public class EnsemblLookup extends EnsemblRestClient
 {
 
+  private static final String OBJECT_TYPE_TRANSLATION = "Translation";
+  private static final String PARENT = "Parent";
+  private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+  private static final String ID = "id";
+  private static final String OBJECT_TYPE_GENE = "Gene";
+  private static final String OBJECT_TYPE = "object_type";
+
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -67,7 +94,7 @@ public class EnsemblLookup extends EnsemblRestClient
   protected URL getUrl(String identifier)
   {
     String url = getDomain() + "/lookup/id/" + identifier
-            + "?content-type=application/json";
+            + CONTENT_TYPE_JSON;
     try
     {
       return new URL(url);
@@ -102,10 +129,10 @@ public class EnsemblLookup extends EnsemblRestClient
    * @param identifier
    * @return
    */
-  public String getParent(String identifier)
+  public String getGeneId(String identifier)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
-  
+
     BufferedReader br = null;
     try
     {
@@ -114,7 +141,7 @@ public class EnsemblLookup extends EnsemblRestClient
       {
         br = getHttpResponse(url, ids);
       }
-      return (parseResponse(br));
+      return br == null ? null : parseResponse(br);
     } catch (IOException e)
     {
       // ignore
@@ -135,8 +162,10 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Parses "Parent" from the JSON response and returns the value, or null if
-   * not found
+   * Parses the JSON response and returns the gene identifier, or null if not
+   * found. If the returned object_type is Gene, returns the id, if Transcript
+   * returns the Parent. If it is Translation (peptide identifier), then the
+   * Parent is the transcript identifier, so we redo the search with this value.
    * 
    * @param br
    * @return
@@ -144,17 +173,42 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   protected String parseResponse(BufferedReader br) throws IOException
   {
-    String parent = null;
+    String geneId = null;
     JSONParser jp = new JSONParser();
     try
     {
       JSONObject val = (JSONObject) jp.parse(br);
-      parent = val.get("Parent").toString();
+      String type = val.get(OBJECT_TYPE).toString();
+      if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+      {
+        geneId = val.get(ID).toString();
+      }
+      else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+      {
+        geneId = val.get(PARENT).toString();
+      }
+      else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+      {
+        String transcriptId = val.get(PARENT).toString();
+        try
+        {
+          geneId = getGeneId(transcriptId);
+        } catch (StackOverflowError e)
+        {
+          /*
+           * unlikely data condition error!
+           */
+          System.err
+                  .println("** Ensembl lookup "
+                          + getUrl(transcriptId).toString()
+                          + " looping on Parent!");
+        }
+      }
     } catch (ParseException e)
     {
       // ignore
     }
-    return parent;
+    return geneId;
   }
 
 }