X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=e425624c2c6cfb5e58596aefc18c44260aca00b0;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=bfae3842b29862a0b0c4a3b1b17a0cae26eb6404;hpb=36dceb54710feb97a81f4bd69ad051f316141dc3;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index bfae384..e425624 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1032,6 +1032,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       // becomes null if the alignment window was closed before the alignment
       // job finished.
       AlignmentI copyComplement = new Alignment(complement);
+      // todo should this be done by copy constructor?
+      copyComplement.setGapCharacter(complement.getGapCharacter());
+      // share the same dataset (and the mappings it holds)
+      copyComplement.setDataset(complement.getDataset());
       copyComplement.alignAs(al);
       if (copyComplement.getHeight() > 0)
       {