JAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS

[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 1ffe27c..4a2a50e 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -5,6 +5,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.MappingType;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.ext.ensembl.EnsemblSeqProxy;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
 
@@ -383,8 +384,7 @@ public class Gff3Helper extends GffHelperBase
     /*
      * Ensembl returns gene name as 'Name' for a transcript
      */
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.TRANSCRIPT))
+    if (EnsemblSeqProxy.isTranscript(sf.getType()))
     {
       desc = StringUtils.listToDelimitedString(attributes.get("Name"), ",");
     }