JAL-2446 merged to spike branch

[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 dc000c6..6d031b7 100644 (file)
--- 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;
+  }
+
 }