From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 14 Mar 2018 14:41:14 +0000 (+0000)
Subject: JAL-2679 reinstating changes lost in VCF merge
X-Git-Tag: Release_2_10_4~44
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=81aed8efd699ef862b29dc638605f23b49ad98d3;p=jalview.git

JAL-2679 reinstating changes lost in VCF merge

Conflicts:
	src/jalview/ext/ensembl/EnsemblLookup.java
---

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 0ddef2b..877331d 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -41,19 +41,6 @@ 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";
-
-  /**
-   * keep track of last identifier retrieved to break loops
-   */
-  private String lastId;
-
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -148,12 +135,11 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
-   * given identifier, or null if not found
+   * Returns the gene id related to the given identifier (which may be for a
+   * gene, transcript or protein)
    * 
    * @param identifier
    * @param objectType
-   *          (optional)
    * @return
    */
   public String getGeneId(String identifier, String objectType)
@@ -163,18 +149,7 @@ public class EnsemblLookup extends EnsemblRestClient
     BufferedReader br = null;
     try
     {
-
       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);