[Bioperl-l] SimpleAlign changes

[Heikki Lehvaslaiho]

I've commited the changes.

Depreciated methods should not be called within bioperl. They will
print a warning if called. There is a remote chance that ClustalW or
TCoffee modules contains some, but I do not have the programs
installed.  Somebody else please check.

As suggested, I did not change the name of the method
Bio::LocatableSeq::get_nse.

Bio::SimpleAlign::purge is the only method left in that package that
needs tests.

The IO methods are now removed. Bio::AlignIO is the only way to io
SimpleAlign alignmets.

I wrote a new, runnable synopsis.

	-Heikki




Hilmar Lapp wrote:
> 
> Heikki Lehvaslaiho wrote:
> >    names. [done] Should depreciated names print a warning? [not done]
> 
> Yes. The rest I think has been answered by Ewan already.
> Excellent, Heikki.
> 
>         Hilmar
> --
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hilmarl@yahoo.com
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
> -----------------------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________