Hi Wim,
Yes, you are absolutely right. The alignment used two different Gap
Symbols. I do not remember the details on this exactly, because the
implementation has been massively changed in the mean time. So, if you
can check out the latest code from the repository, you will find a
version of the alignment algorithms that does use only one kind of Gap
Symbol. The old version cannot be changed or further developed
anymore, sorry. Many changes were necessary to finally ensure that the
Alignment will be gathered in a useful data structure. I strongly
recomment not to use the Alignment from the currently available
release of BioJava but to use the latest version from the SVN
repository. You can do an anonymeous check out by following the
instructions of this web site:
http://biojava.org/wiki/CVS_to_SVN_Migration
I hope this helps!
Best wishes
Andreas
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany
Phone: +49-7071-29-70436
Fax: +49-7071-29-5091
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