[Bioperl-l] Re: sub_Location in Bio::Location::Simple?

[Charles Tilford]

I'm not sure what the Bioperl-culturally-appropriate-interpretation of
"null comment" is - should I add each_location() to the appropriate
modules? Uncertain whether the lack of response indicates quiet
satisfaction or stunned shock...

-CAT

Charles Tilford wrote:
> 
> Jason Stajich wrote:
> 
> >I'd rather create a new method, something like:
> >each_Location().
> >
> >This can be implemented as a recursive method to handle the case when
> >split locations contain other split locations.
> >
> >I don't want to make Simple locations explictly act like Split locations
> >with a single loc since that defeats the purpose of separating the
> >interfaces.
> >
> >Other people may have input?
> >-j
> >
>
> I'm happy with a new method. How about these changes then?
> 
> Bio::Location::Split
> 
> sub each_Location {
>     my ($self, $order) = @_;
>     my @locs = ();
>     foreach my $subloc ($self->sub_Location($order)) {
>     # Recursively check to get hierarchical split locations:
>     push @locs, $subloc->each_Location($order);
>     }
>     return @locs;
> }
> 
> Bio::Location::Simple
> 
> sub each_Location {
>     my ($self) = @_;
>     return $self;
> }
> 
> Bio::LocationI
> 
> sub each_Location {
>     my ($self,@args) = @_;
>     $self->throw_not_implemented();
>     return undef;
> }
> 
> -Charles
> 
> >On Tue, 28 May 2002, Charles Tilford wrote:
> >
> >
> >
> >>Hi Jason,
> >>
> >>Would you mind if I added a sub_Location method in
> >>Bio::Location::Simple? It would look like this:
> >>
> >>=head2 sub_Location
> >>
> >>  Title   : sub_Location
> >>  Usage   : $loc = $loc->sub_Location();
> >>  Function: compatibility method to allow this single method to get
> >>locations from either Simple or Split locations.
> >>  Returns : the Bio::Location::Simple object itself
> >>  Args    :
> >>
> >>=cut
> >>
> >>sub start {
> >>  my ($self) = @_;
> >>  return $self;
> >>}
> >>
> >>I find myself doing this frequently, to grab all the locations in a
> >>given feature:
> >>
> >>        my $fLoc = $feat->location;
> >>        my $locs = ($fLoc =~ /Split/) ? [$fLoc->sub_Location()] : [$fLoc];
> >>
> >>If ::Simple had a sub_Location method, then I could just say:
> >>
> >>my @locs = $feat->location->sub_Location();
> >>
> >>Not sure if I am overlooking a gotcha here...
> >>
> >>-Charles

-- 
Charles Tilford, Bioinformatics-Applied Genomics
Bristol-Myers Squibb PRI, Hopewell 3A039
P.O. Box 5400, Princeton, NJ 08543-5400, (609) 818-3213
charles.tilford@bms.com