I don't know if you got the attachment in my previous email. It contains all DTD
files, sample xml and my simple blastparser file. If not, please check this one
out. I don't think DTD or sample xml has problem because they work for my parser.
Thanks,
Jin
Quoting David Huen <[EMAIL PROTECTED]>:
>
On Sunday 29 Jun 2003 7:00 pm, [EMAIL PROTECTED] wrote:
> Sorry for bothering on this topic again. I have one sample in my zip
> file. My simple XML parser simply works for my sample xml. However, I got
> this error when I try to use your parser:
>
> staxenv [EMAIL PROTECTED]
> org.xml.sax.SAXParse
Sorry for bothering on this topic again. I have one sample in my zip file. My
simple XML parser simply works for my sample xml. However, I got this error when
I try to use your parser:
staxenv [EMAIL PROTECTED]
org.xml.sax.SAXParseException: The markup declarations contained or pointed to
by the d
On Thu, 26 Jun 2003 [EMAIL PROTECTED] wrote:
> I am a little confused. I got your BlastParser.java from WebCVS but didn't find
> any about BlastXMLParserFacade class in that directory. Where should I get that
> file to make BlastParser compiled?
>
> I have written a simple SAX parser for my simpl
I am a little confused. I got your BlastParser.java from WebCVS but didn't find
any about BlastXMLParserFacade class in that directory. Where should I get that
file to make BlastParser compiled?
I have written a simple SAX parser for my simple use. But I am really interested
in how to those handle
On Wednesday 25 Jun 2003 9:24 am, Russell Smithies wrote:
> Hi David,
> Heres the output from a small -m7 blast.
> Ignore the low-scoring hits as I've been toying with a blast db made of
> only binding sites :-)
OK, I've had a look thru' but I don't know what Hsp_pattern-from and
Hsp_pattern-to
On Wed, 25 Jun 2003, Russell Smithies wrote:
> Looks good but doesn't do what I need but I don't think it was ever going to
> :-(
>
> The blast XML data has loads of info in it (I guess thats the reason for the
> format) but I want to be able to get at individual tags, not just hits. For
> examp
Mark
-Original Message-
From: Russell Smithies [mailto:[EMAIL PROTECTED]
Sent: Wed 25/06/2003 4:46 p.m.
To: [EMAIL PROTECTED]; [EMAIL PROTECTED] Org
Cc:
Subject: Re: [Biojava-l] SAX parser demo
Looks good but doesn't
sage -
From: "David Huen" <[EMAIL PROTECTED]>
To: "Russell Smithies" <[EMAIL PROTECTED]>; "[EMAIL PROTECTED]
Org" <[EMAIL PROTECTED]>
Cc: <[EMAIL PROTECTED]>
Sent: Wednesday, June 25, 2003 2:28 PM
Subject: Re: [Biojava-l] SAX parser demo
&g
Hi,
OK, I have uploaded a demo to CVS. It is at biojava-live/demos/blastxml.
It's just a plain ripoff of Mark Schreiber's demo in Biojava In Anger
ported to use the BlastXML parser. You will need to do a "cvs update -d"
to create the new directories for the demos and for the DTD directory.
I
On Tuesday 24 Jun 2003 4:54 am, Russell Smithies wrote:
> It it just me or is Blast's XML screwed?
> I've spent a whole day shagging about but couldn't a SAX parser to
> identify anything but each elements localName :-(
> The Attributes always seem to be empty.
>
> What have I missed?
>
The BJ par
It it just me or is Blast's XML screwed?
I've spent a whole day shagging about but couldn't a SAX parser to identify
anything but each elements localName :-(
The Attributes always seem to be empty.
What have I missed?
Russell
---
import java.io.*;
import
Dear All,
FYI, I've just checked the following classes into the cvs.
In package org.biojava.bio.program.sax:
o An update version of PdbSAXParser.java - more robust parsing of 3-D
molecular structure data
o A new class - NeedleAlignmentSAXParser.java - parsing of multiple
alignments from the pr
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