end<start for empty sequences in Sequence[] from SeqCigar[]

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 08c66d2..3366dcd 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -417,7 +417,7 @@ public class SeqCigar
       SequenceI ref = alseqs[i].getRefSeq();
       seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
                              ref.getStart() + alseqs[i].start+bounds[0],
-                             ref.getStart() + alseqs[i].start+bounds[2]);
+                             ref.getStart() + alseqs[i].start+(bounds[2]==0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
     }
     if (segments!=null) {