Hi -
I would like to be able to add RenderingHints to the various renderers
in BioJava. How can I intercept the Graphics object that is passed to
the Renderers paint(Graphics g, SequencePanel sp) method?
I could overide the method to use the RenderingHints before passing the
arguments to super bu
Wouldn't be a bad place to start anyway.
- Mark
> -Original Message-
> From: Francois Pepin [mailto:[EMAIL PROTECTED]]
> Sent: Tuesday, 14 January 2003 2:00 p.m.
> To: Schreiber, Mark; 'Patrick McConnell'
> Cc: [EMAIL PROTECTED]
> Subject: RE: [Biojava-l] library for running blast and f
On 1/13/03 6:31 PM, "Thomas Down" <[EMAIL PROTECTED]> wrote:
Hey Thomas,
Do you have a doc that describes the functionality in this release??
Something like a feature matrix would be nice to see.
Best,
-B
> We've had a number
I have some code for the running part of it (as java is pretty finicky
about running external apps) on almost any OS.
It's pretty simple (you have to send it the string to be run), but it's
pretty robust and can capture the outputs properly for later use.
If people think that it would be useful t
We've had a number of requests recently for a more recent
snapshot of the biojava-live code, so I've just put together
a biojava-1.3pre1 release. Get source, binaries, and javadocs
from:
http://www.biojava.org/download/
This isn't absolutely set in stone yet, but should give
a reasonable ind
I notice there is a Object call AppBeanRunner that appears to make an
object from an XML file then instantiate it. Is it intended for the type
of activity below or something else?
- Mark
> -Original Message-
> From: Wiepert, Mathieu [mailto:[EMAIL PROTECTED]]
> Sent: Tuesday, 14 January
On 1/13/03 3:19 PM, "Wiepert, Mathieu" <[EMAIL PROTECTED]> wrote:
This functionality exists in the OmniGene Analysis Engine! (OAE). I could
help you get up and running if you are interested.
-B
> It would be good if a command could be described somehow (XML file?)
It would be good if a command could be described somehow (XML file?), and the
interface could query that to find commands, limits, parameter acceptable values,
location of programs maybe? Short of the commands being self-describing, and you knew
where they all were, that might not be so bad? S
One thing sorely missing from BioJava is the ability to launch and
capture the results of common bioinformatics programs. I know Java isn't
the best at this but it's not that bad. It's also needed if you want to
develop pipeline type applications.
Would it be possible to get some kind of over-arch
>I suppose it's a matter of another external dependency vs. reinvented
>utility code in biojava . . . Would it make sense to merge the better
>qualities of the two?
The CLI project looks like it is quite flexible and robust. But, with
this, it is somewhat complex. This is in contrast to the s
On Mon, Jan 13, 2003 at 04:52:14AM -0800, Ethan Cerami wrote:
>
> Right now, I am just modifying the code to display
> exons. The complete code is below. And, I am using
> the following jar file: biojava-20020823.jar.
If you're using that snapshot, you might want to update
to the latest and gre
Hi Everyone,
I am new to BioJava, and had a few questions regarding
rendering of features. First off, I started with the
feature rendering code from BioJava in Anger (thanks
for doing this -- these cookbook recipes are
enormously helpful.)
Right now, I am just modifying the code to display
exons
Also, if you make all the fields public, you can use
it like a struct rather than a bean:
public class Stree {
public Stree left = null;
public Stree right = null;
public Stree parent = null;
public float dist;
public short leaf;
public int order;
public String name;
}
Hi Zhen,
For both the forwards and backwards algorithms, you
can call them in the same way as viterbi. This will
just give you back the score. You can also call them
with an explicit dynamic programming matrix. In this
case, you get the matrix back with all the values
filled in. Both Forward and B
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