X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=dc000c6560bda82680c146edaea6931cdc73fa0d;hb=7aca66e59435c61ed5f5ccfc23734e480e3955d9;hp=856be744d8ea8637b28ea6d7654cfe81be33b31e;hpb=6c52cc0b81ae3abdc3c5f6f88a23364a0246351a;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 856be74..dc000c6 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,12 +1,29 @@
+/*
+ * 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.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
-import java.util.Arrays;
-import java.util.List;
-
 import com.stevesoft.pat.Regex;
 
 /**
@@ -19,9 +36,6 @@ import com.stevesoft.pat.Regex;
  */
 public class EnsemblCdna extends EnsemblSeqProxy
 {
-  private static final List<String> CROSS_REFERENCES = Arrays
-          .asList(new String[] { "Uniprot/SWISSPROT", "Uniprot/SPTREMBL" });
-
   /*
    * accepts ENST or ENSTG with 11 digits
    * or ENSMUST or similar for other species
@@ -29,7 +43,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
    */
   private static final Regex ACCESSION_REGEX = new Regex(
           "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
-  
+
   /*
    * fetch exon features on genomic sequence (to identify the cdna regions)
    * and cds and variation features (to retain)
@@ -114,12 +128,4 @@ public class EnsemblCdna extends EnsemblSeqProxy
     return false;
   }
 
-  @Override
-  protected List<String> getCrossReferenceDatabases()
-  {
-    return CROSS_REFERENCES;
-    // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
-    // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
-  }
-
 }