[Bioperl-l] Re: Bio::SeqIO::bsml.pm

[Ewan Birney]

On Wed, 14 Nov 2001, Charles Tilford wrote:

> All the legal paperwork has finally come in, so I have committed to
> bioperl-live the SeqIO module for converting bioseq objects to and
> from BSML XML files. It's under SeqIO::bsml.pm.
> 
> The module will break with the new Annotation::Collection system,
> which is not 100% backwards compatible - the problems I've encountered
> are:
> 
> * description crashes if there is no description entry present and a
> ->value call is made on undef
> 
> * Annotation.pm would accept an array of references and would add them
> all, the Collection will just add the first one
> 
> * Annotation.pm would allow empty arguments to be passed (for example,
> an empty array to add_Reference, which would then do nothing), whereas
> Collection will throw that it expects to see an object at
> add_Annotation.
> 
> Ewan, do you mind if I make modifications to the backwards-compatible
> methods in Collection.pm to address these? I am uncertain how tolerant
> you wanted the new module to be.

Sure - make it more backward compatible would be great!

> 
> I will make changes in the next few days to bring bsml.pm into full
> compliance with the new Collection system, but in the meantime the 1.1
> revision can be used by anyone with the older Annotation.pm.
> 
> If you want to view BSML files graphically, free viewing software is
> available at:
> 
> http://www.labbook.com/products/standards.asp
> 
> Much of the BSML DTD involves graphical formatting; bsml.pm concerns
> itself almost exclusively with transfering data, so the direct output
> will be somewhat plain.
> 
> Let me know of any issues seen with the code...
> 
> Thanks,
> Charles
> 
>