From 8ab24374eabe70d3d55bc92bcbbae401c743baa5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 14 Mar 2018 14:41:14 +0000
Subject: [PATCH 1/1] JAL-2679 reinstating changes lost in VCF merge

---
 src/jalview/ext/ensembl/EnsemblLookup.java |   89 +++++++++++++++++++++++++---
 1 file changed, 82 insertions(+), 7 deletions(-)

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index e55605d..ed1b4fa 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -47,12 +47,6 @@ import org.json.simple.parser.ParseException;
 public class EnsemblLookup extends EnsemblRestClient
 {
   private static final String SPECIES = "species";
-  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
@@ -149,7 +143,88 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getGeneId(String identifier)
   {
-    return parseGeneId(getResult(identifier, null));
+    return getGeneId(identifier, null);
+  }
+
+  /**
+   * Returns the gene id related to the given identifier (which may be for a
+   * gene, transcript or protein)
+   * 
+   * @param identifier
+   * @param objectType
+   * @return
+   */
+  public String getGeneId(String identifier, String objectType)
+  {
+    List<String> ids = Arrays.asList(new String[] { identifier });
+
+    BufferedReader br = null;
+    try
+    {
+      URL url = getUrl(identifier, objectType);
+      if (url != null)
+      {
+        br = getHttpResponse(url, ids);
+      }
+      return br == null ? null : parseResponse(br);
+    } catch (IOException e)
+    {
+      // ignore
+      return null;
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+  }
+
+  /**
+   * 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
+   * @throws IOException
+   */
+  protected String parseResponse(BufferedReader br) throws IOException
+  {
+    String geneId = null;
+    JSONParser jp = new JSONParser();
+    try
+    {
+      JSONObject val = (JSONObject) jp.parse(br);
+      String type = val.get(OBJECT_TYPE).toString();
+      if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+      {
+        // got the gene - just returns its id
+        geneId = val.get(JSON_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 geneId;
   }
 
   /**
-- 
1.7.10.2