Reverse Complement utility, Bio::Alg, return value problem

[Steve A. Chervitz]

On Wed, 6 Aug 1997, Georg Fuellen wrote:

> 
> I agree w/ SteveC -re- a web driver (see today's post).
> I've already got a little experience using Bio::UnivAln with
> CGI.pm and PGPLOT, see 
> http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/UnivAln/t/univaln.cgi
> (the script is kinda dated, e.g. I've now got a much better grip of PGPLOT)
> Do you think this is on the right track ?
> Anyway, we should keep in mind that for the GUI, we're probably
> going to have Java applets, too -- and then we can also demonstrate that Perl is
> an excellent glue for all this.

Georg, can you install this cgi at your site so we can try it out? It 
looks fine "on paper". Getting Java involved is fine, too, but we need to 
be careful about what is being done by Perl and what is being done by 
Java. For the basic module driver I'm imagining, it would be best to have 
no Java, (unless this is essential for the module).


> > You might want a different name than Bio::Alg, since this name to me 
> > implies that the module *provides* the algorithms rather than simply 
> > wraps around them. Perhaps AlgManager? AlgWrapper?
> 
> I agree; IMO AlgMgr is best.
> (SteveC: If you think your GCG.pm is worth looking at, pls mail it
> or point to it.)

You can take a look at:
http://genome-www.stanford.edu/~sac/perlOOP/bioperl/lib/Bio/Util/GCG.pm

It's and evolving slowly. I'm not very satisfied with it in it's present 
condition but I added some comments to help explain things a bit. 

Cheers,
Steve