[Biojava-l] handling gap symbols

[Andreas Dräger]

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