JAL-1705 compute peptide variants from dna; add "consequence" feature on

[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 55a0f9a..d878f64 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -374,14 +374,10 @@ public class Gff3Helper extends GffHelperBase
     if (SequenceOntology.getInstance().isSequenceVariant(sf.getType()))
     {
       /*
-       * Ensembl returns alleles and consequence_type (amongst other details)
+       * Ensembl returns dna variants as 'alleles'
        */
-      String alleles = StringUtils.listToDelimitedString(
+      desc = StringUtils.listToDelimitedString(
               attributes.get("alleles"), ",");
-      String consequence = StringUtils.listToDelimitedString(
-              attributes.get("consequence_type"), ",");
-      desc = String.format("alleles %s;  consequence %s", alleles,
-              consequence);
     }
     return desc;
   }