JAL-2738 correct handling of reverse strand genes

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cf1cf94..a619d84 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -679,9 +679,10 @@ public class Sequence extends ASequence implements SequenceI
         boolean forwardStrand = "1".equals(tokens[5]);
         String species = ""; // dunno yet!
         int[] from = new int[] { start, end };
-        int[] to = new int[] { chStart, chEnd };
+        int[] to = new int[] { forwardStrand ? chStart : chEnd,
+            forwardStrand ? chEnd : chStart };
         MapList map = new MapList(from, to, 1, 1);
-        GeneLoci gl = new GeneLoci(species, ref, chrom, map, forwardStrand);
+        GeneLoci gl = new GeneLoci(species, ref, chrom, map);
         setGeneLoci(gl);
       } catch (NumberFormatException e)
       {