JAL-2738 unit test for reverse strand gene

[jalview.git] / src / jalview / ext / ensembl / EnsemblGene.java

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index f975ac8..5e970b1 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -426,10 +426,10 @@ public class EnsemblGene extends EnsemblSeqProxy
    * @param mapping
    *          the mapping from gene to transcript positions
    */
-  protected void mapTranscriptToChromosome(Sequence transcript,
+  protected void mapTranscriptToChromosome(SequenceI transcript,
           SequenceI gene, MapList mapping)
   {
-    GeneLoci loci = ((Sequence) gene).getGeneLoci();
+    GeneLoci loci = gene.getGeneLoci();
     if (loci == null)
     {
       return;
@@ -448,8 +448,9 @@ public class EnsemblGene extends EnsemblSeqProxy
 
     List<int[]> exons = mapping.getFromRanges();
     List<int[]> transcriptLoci = new ArrayList<>();
-    
-    for (int[] exon : exons) {
+
+    for (int[] exon : exons)
+    {
       transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
     }