X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=6d031b7e8219222d93a3e41e17cbf208147aab8a;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=dc000c6560bda82680c146edaea6931cdc73fa0d;hpb=8677e6e34e291edc58c1da2fc9c958473754143f;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index dc000c6..6d031b7 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -24,6 +24,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
+import java.util.HashMap;
+import java.util.Map;
+
 import com.stevesoft.pat.Regex;
 
 /**
@@ -44,6 +47,13 @@ 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)
@@ -128,4 +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 Map<String, String> getAdditionalParameters()
+  {
+    return params;
+  }
+
 }