Is there some individual responsible for these bioinf apps emmitting
badly-formed XML that we can shoot very publicly at a conference as a
warning to all others?
(grins)
Matthew
David Huen wrote:
On Wed, 9 Jul 2003, DeAngelo Lampkin wrote:
Hi guys,
First of all, thanks to Keith and Matthew
Hi,
After I have successfully created and initialized a profile HMM, I try to
register the model with a new DP object as follows:
DP dp = DPFactory.DEFAULT.createDP(profile);
This causes the program to hang. Any ideas why this may not work?
Thanks,
Henry Romijn
___
Is PDB file import working?
Invoking:
SequenceFormat sf = SeqIOTools.getSequenceFormat(SeqIOConstants.PDB);
Returns:
org.biojava.bio.BioException: No SequenceFormat available for
format/alphabet identifier '524309'
Anyone else has this problem?
Vasa
_
Hi,
I have narrowed down the problem in creating a dp object for a profile HMM to a
possible bug in the code below from the DP class. I could really use some help
here..
Thanks,
Henry Romijn
public static State[] stateList(MarkovModel mm)
throws IllegalSymbolException, IllegalTransitionE
Dear Sr/Madam,
I am trying to build NetBSD package for biojava1.3, and I want to build
everything from source so when this package is ported to some other OS, it
still work.
Could you please tell me how I can get source codes for bytecode.jar,
xerces.jar, jakarta-regexp.jar & htmlparser.jar?
than
On Thursday 10 Jul 2003 4:53 pm, Yu Wang wrote:
> Dear Sr/Madam,
>
> I am trying to build NetBSD package for biojava1.3, and I want to build
> everything from source so when this package is ported to some other OS,
> it still work.
> Could you please tell me how I can get source codes for bytecode.
Once upon a time, Yu Wang wrote:
> Dear Sr/Madam,
>
> I am trying to build NetBSD package for biojava1.3, and I want to build
> everything from source so when this package is ported to some other OS, it
> still work.
> Could you please tell me how I can get source codes for bytecode.jar,
> xerces.
> "Vasa" == Vasa Curcin <[EMAIL PROTECTED]> writes:
Vasa> Is PDB file import working? Invoking:
Vasa> SequenceFormat sf =
Vasa> SeqIOTools.getSequenceFormat(SeqIOConstants.PDB);
Vasa> Returns:
Vasa> org.biojava.bio.BioException: No SequenceFormat available
Vasa> for
Shooting them would be too kind. A crueler punishment would be to force them to
actually use it. Of course any mind diabolical enough to emit XML like that might
actually take pleasure in such a thing. :)
-Original Message-
From: Matthew Pocock [mailto:[EMAIL PROTECTED]
Sent: Thursday,
Thanks David and Mark,
Mark's email:
>See the JavaDoc comments on
>org.biojava.bio.program.sax.blastxml.BlastOutputHandler for various
>options and a script you could use. Whew that's a long package name :)
Tried to look for this in the JavaDocs on the biojava website, but couldn't find the
c
On Thu, 10 Jul 2003, DeAngelo Lampkin wrote:
>
> >I would strongly recommend using the BlastXMLParserFacade class instead of
> >the BlastXMLParser class unless setting up StAX parsers appeals to you.
> >There is a demo of the use of the latter in the biojava-live repository.
>
> I looked everywh
Hi Henry -
It's difficult to know without knowing how you made the model. The code
example in BioJava in Anger
http://www.biojava.org/docs/bj_in_anger/profileHMM.htm worked last time
I tried. It could be that the ProfileHMM has not been properly
initialized. It could also be a real bug :)
If the
I don't know is BioJava has a PDB reader, I know there is a PDB to XML
type of converter but it seems a shame to not have some way to read PDB
(it keeps us very sequence centric). Does anyone have one they want to
donate?
- Mark
> -Original Message-
> From: Keith James [mailto:[EMAIL PRO
> Tried to look for this in the JavaDocs on the biojava
> website, but couldn't find the class(and after all that
> typing too!). That's when I noticed that those were the docs
> for the pre-release of 1.3. But the class was indeed in the
> 1.3 official release.
>
Hmm, BioJava 1.3 only has
I have vague memories of checking in htmlparser.jar when someone droped
something in CVS that needed it and CVS broke for a while. It is open
source and I found it by doing a google search, not sure where though.
The package name is com.kizna.html so probably it comes from
www.kizna.com I can't fin
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