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

[Heikki Lehvaslaiho]

Charles,

I think silence indicates indifference/inability to see the need of the 
addition/inability to to see any reason to object. You have the need, so do 
the additions and let's see if someone complains.

	-Heikki

Charles Tilford wrote:
> 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
>>>
> 


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       _/      _/                      http://www.ebi.ac.uk/mutations/
      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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