<div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 5, 2015 at 1:18 PM, 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>I know Indeed. But actually my module is not just a parser, it is part of an Input/output system for search results, I think biojava actually lacks this.</div></div></div></blockquote><div><br></div><div>Perhaps others want to chime in if they see the need for this? </div><div><br></div><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> As seen in other Bio projects, aside with Sequence IO and Alignment IO procedures it could have a Search result IO also.<br></div></div></div></blockquote><div><br></div><div>I never understood why other Bio* projects have special Blast modules. Perhaps XML parsing is not as easy as it is in Java? Please see the code at the bottom of this message.</div><div><br></div><div>There is some limited support for calling Blast (and Hmmer) webservices in the webservices module (biojava-ws)</div><div><br></div><div><br></div><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>The advantage is to define common data structures that models Hsp, Hits, Results without taking care (ie. making abstraction) of the underlying search program.<br></div></div></blockquote><div><br></div><div>and the disadvantage is that you constantly need to update them to the variant of blast plus version of the output file format.</div><div><br></div><div> </div><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>And all this work is already done. <br></div></div></blockquote><div><br></div><div>you mean the work has just started :-). Does your module support psiblast, rpsblast, tblastx and blast+ and what versions? </div><div><br></div><div>Take a look at this:</div><div><br></div><div>on the command line, create the Java data model with:</div><div><font face="monospace, monospace">xjc -p blast -dtd "<a href="http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd</a>"</font><br></div><div><br></div><div>and then (slightly shortened)</div><div><br></div><font face="monospace, monospace">JAXBContext jc = JAXBContext.newInstance("blast");<br>Unmarshaller u = jc.createUnmarshaller(); <br>blast.BlastOutput result = (blast.BlastOutput)u.unmarshal(new File("blastoutputfile");</font></div><div class="gmail_quote"><br></div><div class="gmail_quote">Do we really need a special BioJava module for wrapping this?</div><div class="gmail_quote"><br></div><div class="gmail_quote">Andreas</div><div class="gmail_quote"><br></div><div class="gmail_quote"><div><br></div></div><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">-----------------------------------------------------------------------<br>Dr. Andreas Prlic<br>RCSB PDB Protein Data Bank</div><div>Technical & Scientific Team Lead</div><div dir="ltr">University of California, San Diego<div><br></div><div>Editor Software Section <br><div>PLOS Computational Biology<div><div><div><br></div><div>BioJava Project Lead<br>-----------------------------------------------------------------------<br></div></div></div></div></div></div></div></div></div>
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