JAL-2679 use object_type=Transcript for lookup of Parent for Protein

[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 6d031b7..952f01e 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -24,9 +24,6 @@ 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;
 
 /**
@@ -47,13 +44,6 @@ 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)
@@ -139,13 +129,13 @@ public class EnsemblCdna extends EnsemblSeqProxy
   }
 
   /**
-   * Parameter object_type=cdna added to ensure cdna and not peptide is returned
-   * (JAL-2529)
+   * Parameter object_type=Transcaript added to ensure cdna and not peptide is
+   * returned (JAL-2529)
    */
   @Override
-  protected Map<String, String> getAdditionalParameters()
+  protected String getObjectType()
   {
-    return params;
+    return OBJECT_TYPE_TRANSCRIPT;
   }
 
 }