Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch

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

diff --git a/src/jalview/ext/ensembl/EnsemblGenomes.java b/src/jalview/ext/ensembl/EnsemblGenomes.java
index 95acf41..6dd69a8 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGenomes.java
+++ b/src/jalview/ext/ensembl/EnsemblGenomes.java
@@ -1,5 +1,26 @@
+/*
+ * 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.bin.Cache;
 
 /**
  * A class to behave much like EnsemblGene but referencing the ensemblgenomes
@@ -16,25 +37,30 @@ public class EnsemblGenomes extends EnsemblGene
    */
   public EnsemblGenomes()
   {
-    super(ENSEMBL_GENOMES_REST);
+    super();
+    setDomain(Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+            DEFAULT_ENSEMBL_GENOMES_BASEURL));
   }
 
   @Override
-  public boolean isGeneIdentifier(String query)
+  public String getDbName()
   {
-    return true;
+    return "EnsemblGenomes";
   }
 
   @Override
-  public String getDbName()
+  public String getTestQuery()
   {
-    return "EnsemblGenomes";
+    /*
+     * Salmonella gene, Uniprot Q8Z9G6, EMBLCDS CAD01290
+     */
+    return "CAD01290";
   }
 
   @Override
-  public String getTestQuery()
+  public String getDbSource()
   {
-    return "DDB_G0283883";
+    return "EnsemblGenomes";
   }
 
 }