[Biojava-l] handling gap symbols

[Andreas Prlic]

Hi Wim,

I started to play around with snapshot builds for biojava.  So far
(some) of the modules from SVN are available from here:

http://www.biojava.org/download/maven/

Andreas



On Tue, May 25, 2010 at 12:22 AM, Wim De Smet <Wim.DeSmet at ugent.be> wrote:
> 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/
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------