JAL-1705 fetch all Ensembl xrefs (except GO terms)

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

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 5f3f1c8..0ceb29c 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -36,10 +36,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
   private static final String ALLELES = "alleles";
 
-  private static final List<String> CROSS_REFERENCES = Arrays
-          .asList(new String[] { "CCDS", "Uniprot/SWISSPROT",
-              "Uniprot/SPTREMBL" });
-
   protected static final String CONSEQUENCE_TYPE = "consequence_type";
 
   protected static final String PARENT = "Parent";
@@ -316,8 +312,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     }
 
     EnsemblXref xrefFetcher = new EnsemblXref(getDomain());
-    List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName(),
-            getCrossReferenceDatabases());
+    List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
     for (DBRefEntry xref : xrefs)
     {
       seq.addDBRef(xref);
@@ -338,18 +333,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
-   * Returns a list of database names to be used when fetching cross-references.
-   * Specifically, the names are used to filter data returned by the Ensembl
-   * xrefs REST service on the value in field 'dbname'.
-   * 
-   * @return
-   */
-  protected List<String> getCrossReferenceDatabases()
-  {
-    return CROSS_REFERENCES;
-  }
-
-  /**
    * Fetches sequences for the list of accession ids and adds them to the
    * alignment. Returns the extended (or created) alignment.
    *