[Biojava-l] The org.biojava.bio.program.* hierarchy

2001-06-19 Thread Thomas Down
I'm starting to get a little worried about the growth of the bio.program hierarchy. The original contract of this package (and all it's sub-packages) was for wrappers for interacting with external tools. This seems to be stretching thinner and thinner, though... What definitely belongs there:

Re: [Biojava-l] The org.biojava.bio.program.* hierarchy

2001-06-19 Thread Keith James
> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes: Thomas> I'm starting to get a little worried about the growth of Thomas> the bio.program hierarchy. The original contract of this Thomas> package (and all it's sub-packages) was for wrappers for Thomas> interacting with ex

Re: [Biojava-l] The org.biojava.bio.program.* hierarchy

2001-06-19 Thread Thomas Down
On Tue, Jun 19, 2001 at 01:49:34PM +0100, Keith James wrote: > > Related to this, I'm working on Blast/Fasta SAX2 -> Biojava objects > (org.biojava.bio.search.* objects so far, rather than > org.biojava.bio.seq.homol) and was puzzling over where this should > go. Any preferences? Cool. That wou

[Biojava-l] StAX APIs

2001-06-19 Thread Thomas Down
Hi... I've been puzzling for a few weeks now over what to do with the StAX APIs. These are currently living in the BioJava tree, but: - They have absolutely no connection with Biology. And not even that much with Java (the concept could be easily re-implemented in many other languag

[Biojava-l] bootcamp

2001-06-19 Thread Yan Xu
Hi, all, Can anybody kindly tell me some information about Biojava bootcamp? Is it possible to have a copy of the instructions and examples from last bootcamp? Thanks! Best, Yan _ Get your FREE download of MSN Explorer at http://e

Re: [Biojava-l] The org.biojava.bio.program.* hierarchy

2001-06-19 Thread Keith James
> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes: Thomas> On Tue, Jun 19, 2001 at 01:49:34PM +0100, Keith James Thomas> wrote: >> Related to this, I'm working on Blast/Fasta SAX2 -> Biojava >> objects (org.biojava.bio.search.* objects so far, rather than >> org.biojav

[Biojava-l] Primer Picker

2001-06-19 Thread David Waring
Is anyone aware of any Java code related to choosing PCR primers? I have C code for Primer3 from the Whitehead but before I try to write something myself, I just wondered if someone already had. ||| | David Waring | Systems Programmer | U