[Biojava-l] blast/hit/hsp/hspsummary/blastlikealignment objects by using biojava eventbased parser
Bruce Ling
xling@tularik.com
Fri, 7 Sep 2001 08:33:52 -0700
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Hi,
I have done some work on the top of current biojava blast parser. The
implementation of the BlastContentHandler class allows to use the eventbased
parser in biojava to instantiate blast/hit/hsp/hspsummary/blastlikealignment
objects.
It is a very quick implementation following the bioperl ideas such that
the parsing details like xml parser part is hiden from the user such that
the user only needs to deal with the blast/hit/hsp APIs. Because biojava
xml parser has also implemented the parsing of hmmer etc, the extention of
the code to accomodate those should be easy.
Further, extension of the code to parse NCBI blast result should be quick
based upon current code and any xml parser implementing SAX. I should have a
DOM based parser for ncbi xml result very soon as well.
If you want the source code and jar file, just contact me and I will send
you over.
Thanks.
Bruce Ling, Ph.D.
Director, Bioinformatics
Tularik, Inc -- http://www.tularik.com
Email: bruce@tularik.com
Phone: 650-825-7143
fax: 1-435-804-4009
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<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial=20
size=3D2>Hi,</FONT></SPAN></DIV>
<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial size=3D2>I =
have done some=20
work on the top of current biojava blast parser. The implementation of =
the=20
BlastContentHandler class allows to use the eventbased parser in =
biojava to=20
instantiate blast/hit/hsp/hspsummary/blastlikealignment objects. =
</FONT></SPAN></DIV>
<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial size=3D2>It =
is a very quick=20
implementation following the bioperl ideas such that the parsing =
details like=20
xml parser part is hiden from the user such that the user only needs =
to deal=20
with the blast/hit/hsp APIs. Because biojava xml parser has also =
implemented the parsing of hmmer etc, the extention of the code =
to=20
accomodate those should be easy.</FONT></SPAN></DIV>
<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial><FONT =
size=3D2><SPAN=20
class=3D637263315-07092001><FONT=20
color=3D#0000ff> </FONT></SPAN></FONT></FONT></SPAN></DIV>
<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial><FONT =
size=3D2><SPAN=20
class=3D637263315-07092001> </SPAN>Further, extension of the code =
to parse=20
NCBI blast result should be quick based upon current code and any xml =
parser=20
implementing SAX. I should have a DOM based parser for ncbi xml result =
very=20
soon as well.</FONT></FONT></SPAN></DIV>
<DIV><SPAN class=3D070341915-07092001></SPAN><SPAN=20
class=3D070341915-07092001><FONT face=3DArial =
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D070341915-07092001><FONT face=3DArial size=3D2>If =
you want the=20
source code and jar file, just contact me and I will send you=20
over.</FONT></SPAN></DIV><FONT face=3DArial size=3D2></FONT><FONT =
face=3DArial=20
size=3D2></FONT><BR>
<P><FONT size=3D2>Thanks.<BR><BR>Bruce Ling, Ph.D.<BR>Director,=20
Bioinformatics<BR>Tularik, Inc -- <A href=3D"http://www.tularik.com/"=20
target=3D_blank>http://www.tularik.com</A><BR>Email: =
bruce@tularik.com<BR>Phone:=20
650-825-7143<BR>fax: 1-435-804-4009</FONT> </P>
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