The next task is to implement a package retrieving online alignment sequences and return a Bio::SimpleAlign object. The possible way of doing that is to implement these packages:
AlignI.pm (Interface showing methods need to be implemented)
Pfam.pm (Implementation of retrieving alignment data from Pfam)
Uniprot.pm (Implementation of retrieving alignment data from Uniprot)
Probably, in AlignI, the methods are
In the implementation, e.g. Pfam.pm, the package will implement both Bio::DB::Align::AlignI for alignment retrieving methods and Bio::DB::GenericWebAgent for web related methods.
For simplicity, Bio::DB::Align::Pfam and Bio::DB::Align::Uniprot will only implement alignment related methods. The package retrieving other information from these two databases can be implmented later as Bio::DB::Pfam and Bio::DB::Uniprot