X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblProtein.java;h=0280f1613a16c6f17ed32b44ac345364ebd56685;hb=9062c3dbd065631f01af61f47a8cbafabe9c6c8b;hp=97796a5d418a01d6a457cd99a8fc909838e25b14;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index 97796a5..0280f16 100644
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -1,9 +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.AlignmentI;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 
-import java.util.Arrays;
+import java.util.ArrayList;
 import java.util.List;
 
 import com.stevesoft.pat.Regex;
@@ -24,9 +45,6 @@ public class EnsemblProtein extends EnsemblSeqProxy
   private static final Regex ACCESSION_REGEX = new Regex(
           "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
 
-  private static final List<String> CROSSREFS = Arrays.asList(new String[] {
-      "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
-
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -92,16 +110,10 @@ public class EnsemblProtein extends EnsemblSeqProxy
   }
 
   @Override
-  protected boolean identifiesSequence(SequenceFeature sf, String accId)
-  {
-    // not applicable - protein sequence is not a 'subset' of genomic sequence
-    return false;
-  }
-
-  @Override
-  protected List<String> getCrossReferenceDatabases()
+  protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+          String accId)
   {
-    return CROSSREFS;
+    return new ArrayList<>();
   }
 
   @Override