X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblXref.java;h=313572f0639e01419292a35d3464dd232958cb55;hb=e838644df5d5a10a16cf0ad7fb23d24dd7d2729a;hp=514e44a98d86a296cee3fdff83d68a9956faa0b3;hpb=e24933a537e0f640c75d4685c468615872bc77fc;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index 514e44a..313572f 100644
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -27,10 +27,27 @@ import org.json.simple.parser.ParseException;
 class EnsemblXref extends EnsemblRestClient
 {
 
+  private static final String GO_GENE_ONTOLOGY = "GO";
+
+  private String dbName = "ENSEMBL (xref)";
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblXref(String d, String dbSource, String version)
+  {
+    super(d);
+    dbName = dbSource;
+    xrefVersion = dbSource + ":" + version;
+    
+  }
+
   @Override
   public String getDbName()
   {
-    return "ENSEMBL (xref)";
+    return dbName;
   }
 
   @Override
@@ -67,15 +84,14 @@ class EnsemblXref extends EnsemblRestClient
    * Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
    * ("primary_id") for the given identifier (Ensembl accession id) and database
    * names. The "dbname" returned by Ensembl is canonicalised to Jalview's
-   * standard version, and a DBRefEntry constructed. If no databases are
-   * specified, all available cross-references are retrieved.
+   * standard version, and a DBRefEntry constructed. Currently takes all
+   * identifiers apart from GO terms and synonyms.
    * 
    * @param identifier
-   * @param databases
+   *          an Ensembl stable identifier
    * @return
    */
-  public List<DBRefEntry> getCrossReferences(String identifier,
-          List<String> databases)
+  public List<DBRefEntry> getCrossReferences(String identifier)
   {
     List<DBRefEntry> result = new ArrayList<DBRefEntry>();
     List<String> ids = new ArrayList<String>();
@@ -85,11 +101,11 @@ class EnsemblXref extends EnsemblRestClient
     try
     {
       URL url = getUrl(identifier);
-        if (url != null)
-        {
-          br = getHttpResponse(url, ids);
-        }
-      return (parseResponse(br, databases));
+      if (url != null)
+      {
+        br = getHttpResponse(url, ids);
+      }
+      return (parseResponse(br));
     } catch (IOException e)
     {
       // ignore
@@ -112,16 +128,15 @@ class EnsemblXref extends EnsemblRestClient
 
   /**
    * Parses "primary_id" and "dbname" values from the JSON response and
-   * constructs a DBRefEntry if the dbname is in the list supplied. Returns a
-   * list of DBRefEntry created.
+   * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
+   * don't parse "synonyms" as they appear to be either redirected or obsolete
+   * in Uniprot.
    * 
    * @param br
-   * @param databases
    * @return
    * @throws IOException
    */
-  protected List<DBRefEntry> parseResponse(BufferedReader br,
-          List<String> databases)
+  protected List<DBRefEntry> parseResponse(BufferedReader br)
           throws IOException
   {
     JSONParser jp = new JSONParser();
@@ -134,8 +149,7 @@ class EnsemblXref extends EnsemblRestClient
       {
         JSONObject val = (JSONObject) rvals.next();
         String dbName = val.get("dbname").toString();
-        if (databases != null && !databases.isEmpty()
-                && !databases.contains(dbName))
+        if (dbName.equals(GO_GENE_ONTOLOGY))
         {
           continue;
         }
@@ -143,7 +157,7 @@ class EnsemblXref extends EnsemblRestClient
         if (dbName != null && id != null)
         {
           dbName = DBRefUtils.getCanonicalName(dbName);
-          DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
+          DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
           result.add(dbref);
         }
       }
@@ -154,6 +168,18 @@ class EnsemblXref extends EnsemblRestClient
     return result;
   }
 
+  private String xrefVersion = "ENSEMBL:0";
+
+  /**
+   * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
+   * 
+   * @return
+   */
+  public String getXRefVersion()
+  {
+    return xrefVersion;
+  }
+
   /**
    * Returns the URL for the REST endpoint to fetch all cross-references for an
    * identifier. Note this may return protein cross-references for nucleotide.
@@ -164,7 +190,7 @@ class EnsemblXref extends EnsemblRestClient
    */
   protected URL getUrl(String identifier)
   {
-    String url = ENSEMBL_REST + "/xrefs/id/" + identifier
+    String url = getDomain() + "/xrefs/id/" + identifier
             + "?content-type=application/json&all_levels=1";
     try
     {