[Bioperl-l] Sequence Validation

Hilmar Lapp hlapp at gnf.org
Thu Jun 12 11:19:40 EDT 2003

On Thursday, June 12, 2003, at 09:33  AM, Jason Stajich wrote:

> By default the fasta parser uses SeqFastaSpeedFactory which does a 
> direct
> creation of objects bypassing the validation and even the object 
> hierarchy

OK I remember.

Quite frankly I'd like to vote to undo this in the sense that the 
default factory is not a 'speed' factory that does dirty tricks.

Generally speaking I think the strategy should be to do the least 
unexpected thing by default to keep people from being bitten 
unnecessarily. The least unexpected thing obviously may not coincide 
with the fastest way, so there should be documentation for how to make 
bioperl faster if you need it to be faster.

My $0.02.

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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