JAL-1705 add exon name to features and render on peptide (to show

[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 4a2a50e..2e98e4e 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -372,7 +372,9 @@ public class Gff3Helper extends GffHelperBase
       desc = target.split(" ")[0];
     }
 
-    if (SequenceOntology.getInstance().isSequenceVariant(sf.getType()))
+    SequenceOntology so = SequenceOntology.getInstance();
+    String type = sf.getType();
+    if (so.isSequenceVariant(type))
     {
       /*
        * Ensembl returns dna variants as 'alleles'
@@ -382,9 +384,11 @@ public class Gff3Helper extends GffHelperBase
     }
 
     /*
-     * Ensembl returns gene name as 'Name' for a transcript
+     * extract 'Name' for a transcript (to show gene name)
+     * or an exon (so 'colour by label' shows exon boundaries) 
      */
-    if (EnsemblSeqProxy.isTranscript(sf.getType()))
+    if (EnsemblSeqProxy.isTranscript(type)
+            || so.isA(type, SequenceOntology.EXON))
     {
       desc = StringUtils.listToDelimitedString(attributes.get("Name"), ",");
     }