[Bioperl-l] new/unannounced methods

Hilmar Lapp hlapp at gmx.net
Sat Mar 10 12:52:22 EST 2007


On Mar 9, 2007, at 9:55 PM, Chris Fields wrote:

>> Is anyone out there currently working on this? If not I am
>> volunteering.
>> I'd like to move Bio::SeqUtils::trunc_with_features() and friends to
>> Bio::SeqI::trunc(), etc.
>
> I don't think you'll hear too many protests if you want to take it
> on.  Just make sure to add decent tests as needed and document
> everything (one lesson learned from all this!).
>
> The trunc() method is implemented in Bio::PrimarySeqI, so it probably
> should stay there.

Yes, but PrimarySeqI's don't have features.

You could say that it may nevertheless know that there is a derived  
class of Seqs that do. However, why not override the method in, e.g.,  
Bio::SeqI, call the inherited function, and then add whatever is  
needed to truncate the features, too.

	-hilmar

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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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