Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

[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 c7e1d7a..ac4e1d8 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -39,6 +39,8 @@ import java.util.Map;
  */
 public class Gff3Helper extends GffHelperBase
 {
+  public static final String ALLELES = "alleles";
+
   protected static final String TARGET = "Target";
 
   protected static final String ID = "ID";
@@ -214,7 +216,7 @@ public class Gff3Helper extends GffHelperBase
         int fromStart = Integer.parseInt(gffColumns[START_COL]);
         int fromEnd = Integer.parseInt(gffColumns[END_COL]);
         MapList mapping = constructMappingFromAlign(fromStart, fromEnd,
-                toStart, toEnd, MappingType.NucleotideToNucleotide);
+                toStart, toEnd, MappingType.GenomeToCdna);
 
         if (mapping != null)
         {
@@ -399,7 +401,7 @@ public class Gff3Helper extends GffHelperBase
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+      desc = StringUtils.listToDelimitedString(attributes.get(ALLELES),
               ",");
     }