JAL-3076 refactor for more efficient scan of 'gene' features

[jalview.git] / test / jalview / ext / ensembl / EnsemblSeqProxyAdapter.java

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java b/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
index 7077eac..be7bdf2 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
@@ -1,6 +1,30 @@
+/*
+ * 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.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * A convenience class to simplify writing unit tests (pending Mockito or
@@ -8,6 +32,23 @@ import jalview.datamodel.SequenceFeature;
  */
 public class EnsemblSeqProxyAdapter extends EnsemblSeqProxy
 {
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
+  public EnsemblSeqProxyAdapter()
+  {
+    super();
+  }
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblSeqProxyAdapter(String d)
+  {
+    super(d);
+  }
 
   @Override
   public String getDbName()
@@ -28,9 +69,10 @@ public class EnsemblSeqProxyAdapter extends EnsemblSeqProxy
   }
 
   @Override
-  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+          String accId)
   {
-    return false;
+    return new ArrayList<>();
   }
 
 }