Hi Andreas,
Thank you, I'll use that code then. I don't suppose there's a maven
repository that tracks recent dev versions?
regards,
Wim
On 21-05-10 03:56, Andreas Dräger wrote:
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
--
Wim De Smet
http://www.straininfo.net/
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