[Biojava-dev] Fwd: [blast-announce] New Version of BLAST XML output

[Andreas Prlic]

Hi Paolo,

Our policy has been for some time to recommend to create XML output with
BLAST and parse all the required info from there. Due to the excellent
support in Java to parse XML in many different ways we did not feel that
there is a need for providing additional support on top of this in BioJava.

For an example, you could create a data model from the XML schema using xjc and
get an output file parsed into this datamodel using a JAXBContext.

Andreas



On Tue, May 5, 2015 at 7:21 AM, Paolo Pavan <paolo.pavan at gmail.com> wrote:

> Thank you for the advice, Peter.
> By the way, I have a blast parser system extending the biojava one that
> was my intention to submit to the community if it is of any interest.
> If it is so, I can rapidly check it against the new specification sent and
> include it in the main project, If Andreas agree.
>
> Cheers,
> Paolo
>
> 2015-05-05 15:42 GMT+02:00 Peter Cock <p.j.a.cock at googlemail.com>:
>
>> FYI - time to update all the Bio* parsers with the new BLAST XML
>> variant...
>>
>> Peter
>>
>>
>> ---------- Forwarded message ----------
>> From: Mcginnis, Scott (NIH/NLM/NCBI) [E] <mcginnis at ncbi.nlm.nih.gov>
>> Date: Tue, May 5, 2015 at 2:32 PM
>> Subject: [blast-announce] New Version of BLAST XML output
>> To: NLM/NCBI List blast-announce <blast-announce at ncbi.nlm.nih.gov>
>>
>>
>> The NCBI is now making a new version of the BLAST XML available for
>> testing.  Read about the changes and how to access BLAST results using
>> the new XML at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biojava-dev/attachments/20150505/d7c1331a/attachment.html>