X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSequenceFetcher.java;h=bd6335a9f93a042e9308b1e0efe5877ef76ef5ea;hb=4dc7619bed1c475c35f328601b5d7d46116327a6;hp=9a4952e9082d87642432f920f6c208752fd1bea9;hpb=e24933a537e0f640c75d4685c468615872bc77fc;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 9a4952e..bd6335a 100644
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.DBRefSource;
@@ -20,6 +40,10 @@ 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 +55,17 @@ 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 +114,20 @@ 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;
+  }
 }