On Mon, Jan 13, 2003 at 08:10:21PM -0500, Brian Gilman wrote:
> 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.
Now, there's a questio
On Tue, Jan 14, 2003 at 09:40:02AM +1300, Schreiber, Mark wrote:
> 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?
Possibly. The AppBean stuff is very simple, ra
> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes:
Thomas> - Improvements to the handler code for building object
Thomas> models from search results (Keith?). BlastXML support.
Mostly fixes in the search result arena, I think (aside from now using
StAX).
Also
- KMP and re
> "Max" == Markus Roth <[EMAIL PROTECTED]> writes:
Max> hi there, I've been trying to create
Max> SeqSimilaritySearchResults from SAX with the
Max> BlastLikeSearchBuilder. Is there any possibility to get the
Max> MatchConsensus from the Alignment ? or is there nothing
Max>
Hye everyone,
I'm new using Biojava and I have a little problem to solve. I have DNA sequences which
come from sequencing. in these sequences, I have N (ambiguity on a,t,g,c nucleotids).
I'd like to know I could resolve my problem.
I hope someone could answer me
Best regards
Olivier
What I have written provides two essential base classes: Program and
Parameters. The Program class provides the functionality for launching a
program and capturing output. I should also put in hooks for handling the
input and output as streams as an alternative to capturing it in memory.
The Par
Ok, based on the feedback I got yesterday, I have made
much progress :-) Right now, I am trying to create a
bare bones gene viewer that can render gene features
via a SequencePanel object. For example, the code
below renders the Adam2 gene on chromosome 8.
Adam2 is located at: Chromosome 8: 38
On Tue, Jan 14, 2003 at 02:25:13PM +0100, Olivier JEFFROY wrote:
> Hye everyone,
>
> I'm new using Biojava and I have a little problem to solve. I have DNA sequences
>which come from sequencing. in these sequences, I have N (ambiguity on a,t,g,c
>nucleotids). I'd like to know I could resolve my
On 1/14/03 4:56 AM, "Thomas Down" <[EMAIL PROTECTED]> wrote:
Hey Guys,
This has been written a million times before! It exists as a very nice
package on the jakarta apache web site in the "commons" called Digester.
Take a look.
Best,
Other designs to consider
Configurable/Configuration
>
>http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configurable.html
>
>http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configuration.html
Parameterizable/Parameters
>
>http://
On Tue, 14 Jan 2003, Michael L. Heuer wrote:
>
> Other designs to consider
>
> Configurable/Configuration
>
> >
>http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configurable.html
> >
>http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/C
Last one, I promise.
There's also
Commons Configuration project
> http://jakarta.apache.org/commons/sandbox/configuration/index.html
michael
On Tue, 14 Jan 2003, Michael L. Heuer wrote:
>
> On Tue, 14 Jan 2003, Michael L. Heuer wrote:
>
> >
> > Other designs to consider
> >
> > Configura
Thanks for all of the comments/suggestions. There appear to be alot of
libraries out there that deal with parameterization, configuration,
launching external programs, etc. And, they all appear to do it somewhat
differently.
I have completed more work on my lilbrary for launching applications.
Also,
There has been major work done on the Annotation API
ABI, RefSeq and Unigene parsing
Serialization seems pretty stable now
Rework of the Phred package to make the Phred Alphabet more sensible and
Phred Sequence much more elegant.
Circular Sequence coordinates/ locations are much better hande
Hi -
In this case, rather than using the SequencePanel you would use a
TranslatedSequencePanel which allows you to translate (offset) the
coordinates to display the bit you want.
- Mark
> -Original Message-
> From: Ethan Cerami [mailto:[EMAIL PROTECTED]]
> Sent: Wednesday, 15 January 2
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,
I am very interested in helping out with some open source projects that are
going on in order to get more experience in this field. Anyone needs any
help?
Thanks
Art
[EMAIL PROTECTED]
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http://bio
Hi -
Help is always welcome, perhaps if you outline what you are experienced
at and what you would like to do with biojava.
Regards
- Mark
> -Original Message-
> From: Art Sedighi [mailto:[EMAIL PROTECTED]]
> Sent: Wednesday, 15 January 2003 11:19 a.m.
> To: [EMAIL PROTECTED]
> Subject
Hi Mark, et. al.
I have a strong background in Software Engineering which mostly includes
software architecture, design, and implementation. I can go pretty much
anything, but GUI stuff...
I hope this helps...
Thanks
Art
- Original Message -
From: "Schreiber, Mark" <[EMAIL PROTECTED]>
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