Merge remote-tracking branch 'origin/bug/JAL-2722' into portforward/JAL-2675_2102b1to2103

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

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 028492e..6d031b7 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,10 +1,31 @@
+/*
+ * 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.List;
+import java.util.HashMap;
+import java.util.Map;
 
 import com.stevesoft.pat.Regex;
 
@@ -25,7 +46,14 @@ public class EnsemblCdna extends EnsemblSeqProxy
    */
   private static final Regex ACCESSION_REGEX = new Regex(
           "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
-  
+
+  private static Map<String, String> params = new HashMap<String, String>();
+
+  static
+  {
+    params.put("object_type", "transcript");
+  }
+
   /*
    * fetch exon features on genomic sequence (to identify the cdna regions)
    * and cds and variation features (to retain)
@@ -110,12 +138,14 @@ public class EnsemblCdna extends EnsemblSeqProxy
     return false;
   }
 
+  /**
+   * Parameter object_type=cdna added to ensure cdna and not peptide is returned
+   * (JAL-2529)
+   */
   @Override
-  protected List<String> getCrossReferenceDatabases()
+  protected Map<String, String> getAdditionalParameters()
   {
-    return super.getCrossReferenceDatabases();
-    // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
-    // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
+    return params;
   }
 
 }