Re: blast parser

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Biojava 1.7 seems like an ancient version. Did you try 1.9.3 from the
biojava-legacy project? Or even better 5.0.2, the latest current release?

Jose

On Fri, May 25, 2018 at 9:40 AM, Carlos M. Mart=C3=ADnez Ortiz <
[email protected]> wrote:

> Hi, I have implemented a code using the recipe of BiojavaHowTo to parse a
> BLAST output in xml. I=C2=B4m using netbean IDE and biojava-1.7.jar libra=
ry.
> This is the error:
>
> org.xml.sax.SAXException: Could not recognise the format of this file as
> one supported by the framework.
>
>                 At org.biojava.bio.program.sax.BlastLikeSAXParser.parse(
> BlastLikeSAXParser.java:185)
>
>                 at javaapplication1.BlastParser.main(BlastParser.java:41)
>
>
>
> the line 41 is:
>
> parser.parse(new InputSource(is));
>
>
>
> Any help? Thanks you
>
> _______________________________________________
> Biojava-l mailing list  -  [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>

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<div dir=3D"ltr">Biojava 1.7 seems like an ancient version. Did you try 1.9=
.3 from the biojava-legacy project? Or even better 5.0.2, the latest curren=
t release?<div><br></div><div>Jose</div></div><div class=3D"gmail_extra"><b=
r><div class=3D"gmail_quote">On Fri, May 25, 2018 at 9:40 AM, Carlos M. Mar=
t=C3=ADnez Ortiz <span dir=3D"ltr">&lt;<a href=3D"mailto:[email protected]=
u" target=3D"_blank">[email protected]</a>&gt;</span> wrote:<br><blockquo=
te class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc so=
lid;padding-left:1ex"><div lang=3D"ES" link=3D"#0563C1" vlink=3D"#954F72"><=
div class=3D"m_645740501395036168WordSection1"><p class=3D"MsoNormal"><span=
 lang=3D"EN-US">Hi, I have implemented a code using the recipe of BiojavaHo=
wTo to parse a BLAST output in xml. I=C2=B4m using netbean IDE and biojava-=
1.7.jar library.=C2=A0 This is the error:<u></u><u></u></span></p><p class=
=3D"MsoNormal"><span lang=3D"EN-US">org.xml.sax.SAXException: Could not rec=
ognise the format of this file as one supported by the framework.<u></u><u>=
</u></span></p><p class=3D"MsoNormal"><span lang=3D"EN-US">=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
 At org.biojava.bio.program.sax.<wbr>BlastLikeSAXParser.parse(<wbr>BlastLik=
eSAXParser.java:185)<u></u><u></u></span></p><p class=3D"MsoNormal"><span l=
ang=3D"EN-US">=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 at javaapplication1.BlastParser.<wbr>main(Bl=
astParser.java:41)<u></u><u></u></span></p><p class=3D"MsoNormal"><span lan=
g=3D"EN-US"><u></u>=C2=A0<u></u></span></p><p class=3D"MsoNormal"><span lan=
g=3D"EN-US">the line 41 is:<u></u><u></u></span></p><p class=3D"MsoNormal">=
<span lang=3D"EN-US">parser.parse(new InputSource(is));<u></u><u></u></span=
></p><p class=3D"MsoNormal"><span lang=3D"EN-US"><u></u>=C2=A0<u></u></span=
></p><p class=3D"MsoNormal"><span lang=3D"EN-US">Any help? Thanks you <u></=
u><u></u></span></p></div></div><br>______________________________<wbr>____=
_____________<br>
Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]=
en-bio.org">[email protected]</a><br>
<a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l" rel=3D"n=
oreferrer" target=3D"_blank">http://mailman.open-bio.org/<wbr>mailman/listi=
nfo/biojava-l</a><br></blockquote></div><br></div>

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