Merge branch 'releases/Release_2_10_0_Branch'

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index bfae384..c27a4dc 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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)
       {