[Bioperl-l] SeqFeature->_expand_region

[Hilmar Lapp]

On Wednesday, July 2, 2003, at 03:44  PM, Chris Mungall wrote:

> Or maybe the return value for Location::Atomic should be changed
>
>   # let's go ahead and force to '0' if
>   # we are requesting the strand without it
>   # having been set previously
>    return $self->{'_strand'} || 0;
>

I think here is where the offender sits. '0' is defined as 'set to 
unknown', whereas not set is not set.

The expand-logic presently says that adding sub-features can't change 
the knowledge about the strand if there are no coordinates set; 
otherwise (if there are coordinates set) defer that decision to the 
union() implementation.

So, I'd actually argue that if there has been no prior attempt to set 
the strand, the first added subfeature with a strand is allowed to 
promote its knowledge to the container. This is what this piece of code 
does:

     if((! defined($self->start())) && (! defined $self->end())) {
         $self->start($feat->start());
         $self->end($feat->end());
         $self->strand($feat->strand) unless defined($self->strand());

My $0.02.

-hilmar

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