[Bioperl-l] Bio::Seq issue

Roy Chaudhuri roy.chaudhuri at gmail.com
Thu Jun 7 06:42:47 EDT 2012


Hi Paolo,

I received the first patch from the mailing list, so I think you are 
mistaken about the mailer daemon. I agree with Leon that it would be 
better to delegate to Bio::PrimarySeq rather than duplicating the code.

Cheers,
Roy.

On 07/06/2012 11:37, Paolo Pavan wrote:
> No, I didn't already send the patch because the mailer daemon blocked it.
>
> It should be like this, also according to the programming style of the
> PrimarySeq.pm file:
>
> 802,803c802,806
> <  sub is_circular { shift->primary_seq->is_circular }
> <
> ---
>> sub is_circular {
>>      my $self = shift;
>>          return $self->primary_seq->{'is_circular'} = shift if @_;
>>          return $self->primary_seq->{'is_circular'};
>> }
>
>
> 2012/6/7 Leon Timmermans<l.m.timmermans at students.uu.nl>
>
>> On Thu, May 31, 2012 at 5:34 PM, Paolo Pavan<paolo.pavan at gmail.com>
>> wrote:
>>> Do someone agree that they should have the same behaviour?
>>> It the case, attached patch file applied to Bio/Seq.pm file should do the
>>> job.
>>
>> I agree, but your patch is flawed. Peeking and poking into the
>> internals of another object is a bad idea from a maintenance point of
>> view, it should probably look like
>>
>>   sub is_circular { shift->primary_seq->is_circular(@_) }
>>
>> Leon
>>
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