[Bioperl-l] runnable SYNOPSIS + general Analysis client added

[Catherine Letondal]

Heikki Lehvaslaiho wrote:
> 
> One of the first thing most users of a module do is to check the
> SYNOPSIS section of the documentation. The user should be able to copy
> the synopsis or part of, set values to parameters and start building to
> it. 
> 
> I've now made all bioperl core module SYNOPSIS sections runnable.
> Synopsis in 96 modules had to be changed slightly. 
> 
> The new rules for SYNOPSIS:
> 
> 1. It should be possible to copy the whole SYNOPSIS and the perl 
>    compiler should not complain about its syntax. 
> 
> 2. The only exception to the above rule is one line paragraph 
>    linking to a Bio:: module with a relevant synopsis. E.g.:
> 
> =head1 SYNOPSIS
> 
> See L<Bio::DB::GFF>.
> 
> =head DESCRIPTION
> 
> All other comments should be indented (by two spaces) and preceded by
> the hash '#' character. 
> 


1) I have commited a new version for the "static" Pise modules in order
to comply with this documentation rules.

2) I have also added licensing terms similar to perl licensing/redistribution terms.

3) I have changed the -remote parameter to -location, as discussed in
this previous email:

Catherine Letondal wrote (Mon, 03 Mar 2003 23:13:14 +0100):
> 
> Martin Senger wrote:
> > Catherine Letondal wrote:
> > >
> > > -access => 'pise'
> > > could be useful ?
> > >
> >    Absolutely! I have even included Pise in the picture I have drawn (but
> Yes that's right, thanks.
> 
> > I think I have misspelled it, sorry).
> 
> 
> Maybe I should change the -remote parameter of 
> Bio::Tools::Run::AnalysisFactory::Pise class to a -location one, just
> to conform to the Bio::Tools::Run::AnalysisFactory interface ?
> I don't think people already using the Pise API have already used the -remote
> parameter, so it might be still possible to change it.


4) Regarding the "dynamic" modules (277 PiseApplication/*.pm files) :
	- one will be removed (most.pm: the service has been closed)
	- some have changed, but with no impact for the API, except mreps.pm
	(Algorithm for finding maximal tandem repetitions) which has an additional
	parameter
	- the documentation of all modules has changed; in addition to COPYRIGHT, FEEDBACK
	SEE ALSO section, the DESCRIPTION section now contains *only* the parameters
	that can be set by the client. "Fake" parameters such as "Results" or "Paragraph"
	are no longer displayed here.

	=> I have commited only one of this module (genscan.pm) : if this is ok, I will
	commit the others



--
Catherine Letondal -- Pasteur Institute Computing Center