X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=0ddef2b999ef57de300f6c4f511414086bf61a66;hb=d7e95f458ebcbbdcc13f8b07357542ab2d7e4547;hp=4c9ad2b6a7813cef541448e25ef4c2f57a0229bd;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 4c9ad2b..0ddef2b 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;
@@ -14,15 +34,26 @@ 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.
+ * A client for the Ensembl lookup REST endpoint, used to find the gene
+ * identifier given a gene, transcript or protein identifier.
  * 
  * @author gmcarstairs
- *
  */
 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";
+
+  /**
+   * keep track of last identifier retrieved to break loops
+   */
+  private String lastId;
+
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -57,17 +88,26 @@ public class EnsemblLookup extends EnsemblRestClient
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
     String identifier = ids.get(0);
-    return getUrl(identifier);
+    return getUrl(identifier, null);
   }
 
   /**
+   * Gets the url for lookup of the given identifier, optionally with objectType
+   * also specified in the request
+   * 
    * @param identifier
+   * @param objectType
    * @return
    */
-  protected URL getUrl(String identifier)
+  protected URL getUrl(String identifier, String objectType)
   {
     String url = getDomain() + "/lookup/id/" + identifier
-            + "?content-type=application/json";
+            + CONTENT_TYPE_JSON;
+    if (objectType != null)
+    {
+      url += "&" + OBJECT_TYPE + "=" + objectType;
+    }
+
     try
     {
       return new URL(url);
@@ -96,25 +136,50 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
+   * Returns the gene id related to the given identifier, which may be for a
+   * gene, transcript or protein
+   * 
+   * @param identifier
+   * @return
+   */
+  public String getGeneId(String identifier)
+  {
+    return getGeneId(identifier, null);
+  }
+
+  /**
    * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
    * given identifier, or null if not found
    * 
    * @param identifier
+   * @param objectType
+   *          (optional)
    * @return
    */
-  public String getParent(String identifier)
+  public String getGeneId(String identifier, String objectType)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
     BufferedReader br = null;
     try
     {
-      URL url = getUrl(identifier);
+
+      URL url = getUrl(identifier, objectType);
+
+      if (identifier.equals(lastId))
+      {
+        System.err.println("** Ensembl lookup " + url.toString()
+                + " looping on Parent!");
+        return null;
+      }
+
+      lastId = identifier;
+
       if (url != null)
       {
         br = getHttpResponse(url, ids);
       }
-      return (parseResponse(br));
+      return br == null ? null : parseResponse(br);
     } catch (IOException e)
     {
       // ignore
@@ -135,8 +200,10 @@ 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 +211,33 @@ 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))
+      {
+        // got the gene - just returns its id
+        geneId = val.get(ID).toString();
+      }
+      else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+      {
+        // got the transcript - return its (Gene) Parent
+        geneId = val.get(PARENT).toString();
+      }
+      else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+      {
+        // got the protein - get its Parent, restricted to type Transcript
+        String transcriptId = val.get(PARENT).toString();
+        geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+      }
     } catch (ParseException e)
     {
       // ignore
     }
-    return parent;
+    return geneId;
   }
 
 }