Tom Oinn wrote:
You should use : Sequence s =
(Sequence)((DefaultMutableTreeNode)getUserObject()); instead, and next
time read the javadoc for TreeCellRenderer and the like more carefully :)
Or even : Sequence s =
(Sequence)((DefaultMutableTreeNode)value).getUserObject(); in the case
of
Jacob Rohde wrote:
Hi,
I'm having a problem with a JTree and rendering of Sequences.
Since the JTree calls toString() on objects when displaying them, I
had to make my own TreeCellRenderer because the Sequence toString
method prints out debug info.
My code looks like this:
public class Featur
[EMAIL PROTECTED] wrote:
The internal use was mine (I was just using it as a substitute for a
namespace). Maybe we should upgrade it to be compatable with IBM or
Taverna?
- Mark
Michael Heuer <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/16/2005 03:27 AM
To: Gary Bader
Egon Willighagen wrote:
On Tuesday 11 January 2005 11:49 am, Tom Oinn wrote:
Andreas Prlic wrote:
I am the person who contributed the biojava - structure classes. As it
turns out I am a very happy Jmol user already for quite a while now! :-)
Seconded - Jmol is very cool and surprisingly easy to
Andreas Prlic wrote:
Hi Egon!
I am the person who contributed the biojava - structure classes. As it
turns out I am a very happy Jmol user already for quite a while now! :-)
Seconded - Jmol is very cool and surprisingly easy to integrate if you
have PDB format data lying around somewhere in your
Matthew Pocock wrote:
Tom Oinn wrote:
Matthew - you're both on this list and working up at Newcastle, does
this seem reasonable?
Yes. Very.
Let's hope the BBSRC agree :)
I'll be up in a few weeks to talk to the biologists, perhaps we could
get together over a drink or seve
Hi Ralf, Mark, all...
Are you aware of our project, Taverna? We're working with various
groups, mostly up at Newcastle and Manchester but also here at the EBI
to provide workflow based technology for bioinformatics. Specifically,
we have a system, Soaplab, that can wrap arbitrary command line t
Matthew Pocock wrote:
I think what you need to do is write an Axis serializer / deserializer
that understands lists and add that to your soap service - it seems odd
that Axis doesn't come with one bundled like it does for Map.
Um, it does. Either that or my lists have been magically sent by te
they always?) but usable in its current
form. Anyway, sorry if this is off topic too much, we are actually
planning to contribute parts of Soaplab's clients into BioJava in the
same way as we have for BioPerl, and similarly so for the workflow
engine if that's desirable.
Cheers,
Tom O
Isn't this what the ACD files in EMBOSS are doing? Perhaps not
reinventing the wheel would be good? Admittedly ACD is not the most
parsable file format to work with, but we have an XML dialect of it
which is (part of Martin's Soaplab).
Martin - is the XML schema available somewhere? I can't fin
Patrick McConnell wrote:
Forwarded below is another stab at the problem that EBI has made. After
just glancing at the docs, it looks pretty good. And, the developer on the
project (Martin Senger) appears dedicated to moving his code to BioPerl and
BioJava. So, that sounds good to me. Martin
Hi all... there appears to be a '"' missing on
http://www.biojava.org/docs/, could someone with appropriate access
search for
http://www.biodas.org/>DAS client
and replace with
http://www.biodas.org/";>DAS client
Cheers,
Tom
___
Biojava-l mailing
n :)
Cheers,
Tom Oinn
___
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
Keith James wrote:
>
> > "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes:
>
> Matthew> Hi All, Have any of you used beanshell? I'm having a look
> Matthew> at it now, and it appears to be a fairly sensible
> Matthew> java-ish scripting language. Perhaps it would be a pla
Chris Mungall wrote:
>
> On Tue, 19 Mar 2002 [EMAIL PROTECTED] wrote:
>
> > Message: 2
> > From: "Matthew Pocock" <[EMAIL PROTECTED]>
> > To: "Tom Oinn" <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]>
> > Subject: Re: start using
Matthew Pocock wrote:
> Anyone: I don't think we even have a GO client - can this be easily
> rectified?
I'd be happy to put our GO browser and client API into biojava, what
would you need for this to work? I'm guessing that a standard schema
(probably the one used by the stanford people) and
Petri Pehkonen wrote:
>
> Hi,
>
> To be more specific, I'm currently finding the API-documentation and/or
> sourcecode of class org.bdgp.swing.widget.DataAdapterChooser. If you know
> where to find it let me know please!
Have you tried following the links from bdgp.org perhaps? In general if
Matthew Pocock wrote:
>
> Hi.
>
> I've checked in a preliminary taxa implementation to:
>
> org.biojava.bio.taxa
>
> There is a demo at:
>
> demos/seq/TestSwissprotOrg.java
>
> and I've added a seq io object to:
>
> org.biojava.bio.seq.io.OrganismParser
>
> There is some work to do - I t
Matthew Pocock wrote:
>
> Hi.
>
> Does anybody have any strong opinions about taxanomic data in BioJava? I
> was going to pop in a new package org.biojava.bio.taxa with interfaces &
> in-memory implementations of taxonomies. The aim is that this should
> play well with the ebi taxonomy databas
> Ungsik Yu wrote:
>
> Dear Mr. Tom Oinn:
>
> I read your posting on BioJava mailing list.
> I would like to try your EBI InterPro Java API.
> Is it possible to receive the source of the API?
Currently the InterPro and GO APIs are separate, the former being under
devel
ebi.ac.uk/~tmo/ipro4/api
I'd be grateful if someone or someones could take a look and give me
your thoughts on whether it would be sane to integrate this into the
bio* stuff. Anyone on site is welcome to call round and talk more
directly if you're
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