JAL-1705 EnsemblGene added, and related refactoring

[jalview.git] / src / jalview / io / gff / Gff3Helper.java

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index d878f64..1ffe27c 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -379,6 +379,15 @@ public class Gff3Helper extends GffHelperBase
       desc = StringUtils.listToDelimitedString(
               attributes.get("alleles"), ",");
     }
+
+    /*
+     * Ensembl returns gene name as 'Name' for a transcript
+     */
+    if (SequenceOntology.getInstance().isA(sf.getType(),
+            SequenceOntology.TRANSCRIPT))
+    {
+      desc = StringUtils.listToDelimitedString(attributes.get("Name"), ",");
+    }
     return desc;
   }
 }