[Biopython-dev] Bio.AlignIO

[Peter]

Michiel de Hoon wrote:
> Sure, that is possible, but that means we'd be adding methods to 
> Alignment in order for it to behave like a list, whereas we can get 
> that for free by letting the Alignment class inherit from list.
> 
> --Michiel.

Personally I see an alignment as both an array of characters (i.e. amino 
acid residues or nucleotides), and a list of sequences.

In the same way that a Numeric or NumPy array lets you iterate over 
rows, yet also access individual elements, we could allow iteration of 
SeqRecords and also allow access to individual letters.

Peter