[Bioperl-l] Re: [Root-l] new Bioperl bug tracking system

[Ewan Birney]

>
> So the thing I wanted was this little subtle difference:
> my $seq = new Seq(-storage => "disk");
>

;) Right, but this doesn't work here:

my $storage_type = shift; # read from argv

# Doh! this wont work for storage_type disk because the whole
# point is that we can't get this into memory!
my $seq = new Seq ( -storage => $storage_type, -seq => $string);


ie - the point is that we can't nicely hide anything behind run-time
interfaces - the best we can do is put in the SeqIO LargeFasta loader
which is hidden behind the SeqIO class.


when we can hide things from the client (eg. SeqIO, SearchIO, Bio::DB::*)
we do - probably should do more of this, but you have chosen an example
where we really do need to client to give us some hints...