<div dir="ltr">Hi Paolo,<div><br></div><div>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. </div><div><br></div><div>For an example, you could create a data model from the XML schema using <span style="color:inherit;font-family:Menlo,Monaco,Consolas,'Courier New',monospace;font-size:inherit;line-height:18.5714302062988px;white-space:pre-wrap;background-color:transparent">xjc</span> and get an output file parsed into this datamodel using a JAXBContext.</div><div><br></div><div>Andreas</div><div><br></div><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 5, 2015 at 7:21 AM, Paolo Pavan <span dir="ltr"><<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div>Thank you for the advice, Peter.<br>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. <br></div>If it is so, I can rapidly check it against the new specification sent and include it in the main project, If Andreas agree.<br><br></div>Cheers,<br></div>Paolo<br></div><div class=""><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2015-05-05 15:42 GMT+02:00 Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">FYI - time to update all the Bio* parsers with the new BLAST XML variant...<br>
<br>
Peter<br>
<br>
<br>
---------- Forwarded message ----------<br>
From: Mcginnis, Scott (NIH/NLM/NCBI) [E] <<a href="mailto:mcginnis@ncbi.nlm.nih.gov" target="_blank">mcginnis@ncbi.nlm.nih.gov</a>><br>
Date: Tue, May 5, 2015 at 2:32 PM<br>
Subject: [blast-announce] New Version of BLAST XML output<br>
To: NLM/NCBI List blast-announce <<a href="mailto:blast-announce@ncbi.nlm.nih.gov" target="_blank">blast-announce@ncbi.nlm.nih.gov</a>><br>
<br>
<br>
The NCBI is now making a new version of the BLAST XML available for<br>
testing. Read about the changes and how to access BLAST results using<br>
the new XML at <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf</a><br>
_______________________________________________<br>
biojava-dev mailing list<br>
<a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
</blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
biojava-dev mailing list<br>
<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br></blockquote></div><br><div><br></div>
</div></div></div>