[Biojava-l] Alignment/ Alphabet issues (was biojava v2 alpha1 release)

[mark.schreiber at group.novartis.com]

Hi John -

if you get source from BioJava live or a recent snapshot it should be able 
to handle gap counting in Alignments via DistributionTools various 
distributions form alignment methods. It is done through a very dodgey 
hack that hopefully is not needed in BJ2 (or is at least formalized so 
anyone can do it). Gaps are not too well handled in BJ1. They sort of are 
and are not part of the alphabet.

I am also working on a generalized wrapper to allow soft masking of an 
alphabet as well as a SymbolTokenization that understands how to deal with 
it. Should be done soon if there is interest but it would be better 
handled at a more core level if possible in BJ2.

On the subject of LGPL v GPL, having worked in companies for a while 
making biojava GPL would render it unusable for industry. Even if I write 
something that will never be shrinkwrapped and sold no legal team will 
ever allow me to use biojava if it means anything I write has to be GPL. 
We may choose to make it GPL but we don't want to be forced to.

Regards,

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"Osborne, John" <jko1 at cdc.gov>
Sent by: biojava-dev-bounces at portal.open-bio.org
05/06/2004 03:50 AM

 
        To:     "Matthew Pocock" <matthew_pocock at yahoo.co.uk>
        cc:     biojava-dev at biojava.org
        Subject:        RE: [Biojava-dev] biojava v2 alpha1 release


I think lGPL is fine, although I would be happier with the more "viral"
GPL but until I contribute some source I'll try to keep my mouth shut.
:)  I'm just curious though, is anybody out there actually distributing
biojava as part of commerical *commodity* software?  I'm not talking one
of a kind projects that use biojava, but shrinked wrapped software where
source code protection really matters.

Speaking of which, is there a javadoc or download area for bjv2?
(haven't installed subversion)

I've been waiting ages to contribute, but most of the stuff I would put
in is multiple alignment analysis stuff, which is a bit of a mess in
bjv1 (gap character issues, alignment handling code split across
packages, etc...)  Maybe bjv2 is the trick.

 -John



-----Original Message-----
From: biojava-dev-bounces at portal.open-bio.org
[mailto:biojava-dev-bounces at portal.open-bio.org] On Behalf Of Matthew
Pocock
Sent: Wednesday, May 05, 2004 12:58 PM
To: biojava-dev at biojava.org
Subject: [Biojava-dev] biojava v2 alpha1 release


Hi,

I have just committed the alpha1 release of biojava 2 (code-named 
medusa) to svn. To compile & run BJV2, you will need a 1.5 java sdk, SVN

(1.0 or newer) and a reasonably up-to-date ANT. I'm releasing this 
revision under lGPL. I am happy to move to another open-source license 
if people feel it would be helpfull. GPL and OSL appear to be no good - 
to viral. BSD and friends are no good - too easy to split/pilfer. I'm 
reading through licences on http://www.opensource.org/licenses/ in the 
vain hope of finding something suitable.

All bugs/questions either direct to me or to biojava-dev.

Matthew

----

Getting bjv2:

the complete thing
  http://www.derkholm.net/svn/repos/bjv2

development version
  http://www.derkholm.net/svn/repos/bjv2/trunk

alpha1 release
  http://www.derkholm.net/svn/repos/bjv2/branches/medusa

----

Things I want in the license:

1) "we" own the code - a 3rd party can't take it, change the formatting 
and stop us using it

2) "you" can incorporate the library into your app. this requries you
to:
  acknowledge that you use us & what license you use us under
  provide access to the source - presumably as a link to our repository

3) if "you" have modified "our" source and then distribute the 
modification you must:
  notify the user that you've done this
  make the source of the modifications available under this license
  allow the modifications to be rolled back into the main copy of the 
code (we may chose not to though)

4) "you" can use example code without tainting your apps with our
license

5) none of this lGPL linking rubbish - what's that all about anyway?

6) "we" are not liable for anything - we don't claim the code is fit for

any purpose and if it craps out, you pay the consequences

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