On Tue, 12 Aug 2003, Schreiber, Mark wrote:
> Running on a remote machine (ie where the service is located by
> something like JNDI) might be best left to something like J2EE message
> driven beans or something similar. For good old biojava we should
> probably focus (at first) on local. After all
> 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?
Mark -
Thanks for your response to my message.
I am using the netBeans 3.5 IDE for editing and compiling Java files. I
have found that if I mount the biojava-1.30-jdk14.jar archive inside the
IDE, the Java compiler is able to find all the files it needs, even if I
don't edit the Windows PATH var
Once upon a time, Francois Pepin wrote:
> I've added it to the cvs as org.biojava.utils.ExecRunner. It make take a
> little while to be replicated in the anonymous cvs.
Sorry, our two solutions seem to have crossed in cyberspace :-(.
As far as I can tell, ExecRunner has:
- Use of Windows cmd
Well right, I logged in root whatsoever for the
permissions.
[EMAIL PROTECTED] biojava-acedb]# ant
Buildfile: build.xml
init:
prepare:
[mkdir] Created dir:
/home/newton/biojava-acedb/ant-build
prepare-src:
[mkdir] Created dir:
/home/newton/biojava-acedb/ant-build/src
[mkdir] Created
Running on a remote machine (ie where the service is located by something like JNDI)
might be best left to something like J2EE message driven beans or something similar.
For good old biojava we should probably focus (at first) on local. After all once the
local running service is working it can
I have implemented LocalProgram which runs programs based on an XML
description of the parameters. Program IO is handled in separate threads.
Also, local resources, such as paths to executables and databases, can be
loaded from XML. I have made the binaries, source, and documentation
availab
Guys,
Could someone who know acedb take a look at it? I just did a clean
checkout from the cvs and ant still crashed on me.
The build.xml references the resources directory which doesn't exist
(should probably be commented in). It looks like it's missing some
biojava code as well in there. It's g
On Monday 11 Aug 2003 3:03 pm, Francois Pepin wrote:
> I have code that did that, but it wasn't reliable enough to use like
> that. For unknown reasons, there are programs that I couldn't call at
> all.
>
> The only reliable method that I found was to write a one-liner shell
> script to be executed
Hi,
I construct a profile HMM with randomized uniform distributions. I then train
the model and, regardless of the training set I use, it ends up looking like
this:
- a 0.999 probability to go from one delete state to the next
- roughly a uniform emission distribution for emission states (insert
I would tend to agree with Keith. Making hardcoded command lines can loose platform
independence pretty quickly. I would prefer to see users register their own command
lines, preferences etc with some kind of registry object.
- Mark
-Original Message-
From: Keith Jam
I'm looking through the documentation for biojava 1.3, and cannot find
any reference to performing a BLAST search, or performing any type of
SmithWaterman local alignment. If its there, and I'm just not looking
in the right place, can someone please direct me to where I can find
information on thi
Hi Suman,
My guess is that you have a permission problem somewhere, or that your
disk is full or something similar.
Try to see if you can create that directory by yourself.
The error seems to be about being able to create the directory itself.
It happened before any of the code was touched for c
> "Tom" == Tom Oinn <[EMAIL PROTECTED]> writes:
Tom> Isn't this what the ACD files in EMBOSS are doing? Perhaps not
Tom> reinventing the wheel would be good? Admittedly ACD is not the
Tom> most parsable file format to work with, but we have an XML
Tom> dialect of it which is (part of M
I agree - parameters like that would be better to work with
programatically. But, I would like to see the everything done as flexibly
as possible, so that you could pass in an arbitrary parameter. Also, you
should be able to get binary data from stdout/err. Perhaps a ByteBuffer
class should
Hi there,
Apologies for the slight plug, but at the EBI we've been working on
something that might be of interest to people trying to do this. We have
a system called Soaplab that can be used to expose command line tools as
web services (trivial to then consume) and another project Taverna whic
I figured out something that I need to use ant to
build the acedb-biojava, with the build.xml provided
by the package. Now the problem:
[EMAIL PROTECTED] bin]$ ant -buildfile
~/biojava-acedb/build.xml
Buildfile: /home/newton/biojava-acedb/build.xml
init:
prepare:
BUILD FAILED
file:/home/newton/
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
Once upon a time, Patrick McConnell wrote:
>
> Or, even better would be some sort of Parameters class to encapsulate all
> those parameters, providing optional parameters. Then, you could do
> something like this:
>
>NCBIBlastParameters params = new NCBIBlastParameters();
>params.addPara
I'll take care of combining the two, basically adding the ExecRunner
functionality to ProcessTools.
Thomas, how tested is ProcessTools? Is it something that you just wrote
up or is it code that's been found to work flawlessly on different kind
of applications?
Francois.
On Mon, 2003-08-11 at 12:
> I have code that did that, but it wasn't reliable enough to use like
> that. For unknown reasons, there are programs that I couldn't call at
> all.
Do you still have any of those programs lying around? I'd be very much
interested to test if the invocation of problematic command line
applications
Dear biojava-l-request:
Hi, Mark, We are the center of bioinformatics of Peking University (Beijing,P.R.
China) which is national node of
EMBnet. I would like to do the chinese version of biojava in Anger if you agree .
=== 2003-08-11 您在来信中写道：===
>Send Biojava-l mailing list subm
Once upon a time, Ryan Golhar wrote:
> I'm looking through the documentation for biojava 1.3, and cannot find
> any reference to performing a BLAST search, or performing any type of
> SmithWaterman local alignment. If its there, and I'm just not looking
> in the right place, can someone please dir
Once upon a time, Halfdan Rydbeck wrote:
>
> I have been trying to install BioJava on a Windows 2000 machine for a
> day now but cant get it to work.
> Maybe you could help me out here?
>
> I store my .jar-files (biojava-1.30-jdk14, bytecode-0.92,
> jakarta-regexp, xerces) in C:\biojava.
>
> M
Actually, this is the way you're supposed to use JAR files in Netbeans. It's
documented, but badly placed in a non-obvious location(IMO). This causes a lot of
people grief.
-Original Message-
From: David Millis [mailto:[EMAIL PROTECTED]
Sent: Sunday, August 10, 2003 5:10 AM
To: 'Schrei
For maximum flexibility and ease of use, I think describing the parameters
in an external (editable) file would be preferrable. I do not think it
would be too hard to come up with an XML schema for describing how programs
should be run. Something like:
NCBI Blast
default
-
> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes:
[...]
Thomas> Yes, I quite agree. Although I think I'd prefer something
Thomas> more like:
Thomas>params.addParameter(NCBIBlast.PROGRAM_NAME, "blastn")
Thomas> Have you looked at the AnnotationType class? We could
Hi everyone,
I'd like to have people's opinions on some of the changes that I did to
it:
The code has been switched from Input/OutputStreams to Reader/Writer. Do
people want to be able to define a particular charset when the transfer
is done? Right now the default charset is being used.
The code
Dear biojava-l-request:
Yes, I think Mark hits the point. The big problem of biojava (in fact, java) is
how to communicate with other bioinformatic tools. We always have to use java system
api to call the programs we need, but of course it is a drawback.
It will be the bottleneck of biojava if
Hi -
Sounds great! Thomas Down also mentioned that he might know of someone who could help
out. (Thomas could you put these people in touch with each other??)
Let me know when you need me to put pages up or set up links.
- Mark
-Original Message-
From: [EMAIL PROT
On Mon, 2003-08-11 at 11:57, David Huen wrote:
> Would something hybrid like Jython be useful in this context? Perhaps they
> might have encountered and solved some of these problems.
I'd have a preference to an all-java solution if possible. Java code is
easier to maintain for the rest of us.
Once upon a time, Thomas Down wrote:
>
> A lot of these issues could probably be addressed by something
> like:
>
> public class ExecTools {
Okay, I've had a first stab at this -- you can see what I
ended up with in org.biojava.utils.ProcessTools. In my
tests so far, it seems to be working quite
Since 1.4 seems to come bundled with net-beans now,
should we update the docs to say how to get biojava
working in netbeans? Love it or hate it, everyone is
going to have it.
Matthew
--- David Millis <[EMAIL PROTECTED]> wrote: >
Mark -
>
> Thanks for your response to my message.
>
> I am usin
I have code that did that, but it wasn't reliable enough to use like
that. For unknown reasons, there are programs that I couldn't call at
all.
The only reliable method that I found was to write a one-liner shell
script to be executed by sh, but this is an ugly, ugly hack.
The grabbing of stdin a
I've added it to the cvs as org.biojava.utils.ExecRunner. It make take a
little while to be replicated in the anonymous cvs.
It was originally released under the GPL for another project, but I got
permission from the author to add it in biojava under LGPL.
It has the advantage that it's supposed
Hello all,
The unexpectidly popular biojava in anger site has now been translated
into Japanese. A big thanks to the Translators Takeshi Sasayama and
Kentaro Sugino and possibly others, let me know if I haven't credited
every one.
Just follow the link off the main page:
http://www.biojava.org/doc
References: <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]>
<[EMAIL PROTECTED]>
In-Reply-To: <[EMAIL PROTECTED]>
From: "hywang" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: Re: How to Use SixFrameRenderer and related classes?
Date: Thu, 07 Aug 2003 10:49:38 +0800
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