Re: handling gap symbols
Andreas Dräger <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l