JAL-2738 getGeneLoci promoted to SequenceI

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cf1cf94..5d8a3ef 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)
       {
@@ -700,6 +701,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return
    */
+  @Override
   public GeneLoci getGeneLoci()
   {
     return geneLoci;