JAL-2738 use complement base for a VCF variant on 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 32b7c7c..45e8e34 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -429,7 +429,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   protected void mapTranscriptToChromosome(Sequence transcript,
           SequenceI gene, MapList mapping)
   {
-    GeneLoci loci = ((Sequence) gene).getGeneLoci();
+    GeneLoci loci = gene.getGeneLoci();
     if (loci == null)
     {
       return;
@@ -439,7 +439,7 @@ public class EnsemblGene extends EnsemblSeqProxy
      * patch to ensure gene to chromosome mapping is complete
      * (in case created before gene length was known)
      */
-    MapList geneMapping = loci.getMapping();
+    MapList geneMapping = loci.mapping;
     if (geneMapping.getFromRanges().get(0)[1] == 0)
     {
       geneMapping.getFromRanges().get(0)[0] = gene.getStart();
@@ -448,16 +448,17 @@ 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]));
     }
 
     List<int[]> transcriptRange = Arrays.asList(new int[] {
         transcript.getStart(), transcript.getEnd() });
     MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
-    GeneLoci gl = new GeneLoci(loci.getSpecies(), loci.getReference(),
-            loci.getChromosome(), mapList, loci.isForwardStrand());
+    GeneLoci gl = new GeneLoci(loci.species, loci.assembly,
+            loci.chromosome, mapList);
 
     transcript.setGeneLoci(gl);
   }