JAL-1705 add DBRefEntry for 'self' to retrieved transcripts so they are

[jalview.git] / src / jalview / ext / ensembl / EnsemblXref.java

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index f19b4d4..7b5f9da 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -81,7 +81,9 @@ class EnsemblXref extends EnsemblRestClient
    * specified, all available cross-references are retrieved.
    * 
    * @param identifier
+   *          an Ensembl stable identifier
    * @param databases
+   *          optional list of Ensembl cross-referenced databases of interest
    * @return
    */
   public List<DBRefEntry> getCrossReferences(String identifier,
@@ -95,10 +97,10 @@ class EnsemblXref extends EnsemblRestClient
     try
     {
       URL url = getUrl(identifier);
-        if (url != null)
-        {
-          br = getHttpResponse(url, ids);
-        }
+      if (url != null)
+      {
+        br = getHttpResponse(url, ids);
+      }
       return (parseResponse(br, databases));
     } catch (IOException e)
     {
@@ -123,7 +125,8 @@ 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.
+   * 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