// 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)
{