Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 9a4952e..dd1739b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -20,6 +20,10 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
   private static final Regex ACCESSION_REGEX = new Regex(
           "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
 
+  protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+
+  protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+
   /*
    * possible values for the 'feature' parameter of the /overlap REST service
    * @see http://rest.ensembl.org/documentation/info/overlap_id
@@ -31,17 +35,17 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
     constrained, regulatory
   }
 
+  private String domain = ENSEMBL_REST;
+
   @Override
   public String getDbSource()
   {
     // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
-    return DBRefSource.ENSEMBL; // "ENSEMBL"
-  }
-
-  @Override
-  public String getDbVersion()
-  {
-    return "0";
+    if (ENSEMBL_GENOMES_REST.equals(getDomain()))
+    {
+      return DBRefSource.ENSEMBLGENOMES;
+    }
+    return DBRefSource.ENSEMBL;
   }
 
   @Override
@@ -90,4 +94,20 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
   {
     return true;
   }
+
+  /**
+   * Returns the domain name to query e.g. http://rest.ensembl.org or
+   * http://rest.ensemblgenomes.org
+   * 
+   * @return
+   */
+  protected String getDomain()
+  {
+    return domain;
+  }
+
+  protected void setDomain(String d)
+  {
+    domain = d;
+  }
 }