[Bioperl-l] is_remote() in Location::Simple

[Hilmar Lapp]

Elia Stupka wrote:
> 
> > This was my feeling: the utility of this method is tied to some
> > quite specific application and not intuitive anywhere else (a
> 
> I see your point, however the specific application is another bioperl
> module, bioperl-db and in biopeerl-db we don't want to do carry the main
> seqid through many objects, do you have any proposal to solve this?
> 
> I see one simple option, to reimplement is_remote becomes something like
> _is_remote_in_parser, which should make us all happy, how does it sound?
> Other suggestions?
> 

It appears that the concept of parent sequences in terms of locations
applies to sub-locations of a compound (split) location, the issue
being that if such a sub-location is a simple location there is no way
of tracking the parent in the sub-location. Is this correct?

If it is, my suggestion is the following (code obviously slightly
simplified):

package Bio::Location::SubLocationI;
@ISA = qw(Bio::LocationI);

sub parent_seq_id {
	# abstract stub
}

package Bio::Location::SimpleSubLocation;
@ISA = qw(Bio::Location::Simple Bio::Location::SubLocationI);

sub parent_seq_id {
	# implement get/set
}

Similarly, one will probably like to have Location::FuzzySubLocation
and Location::SplitSubLocation, for completeness. The definition of
Location::SplitLocationI::sub_Location() is then changed such that
returned objects can be expected to implement Location::SubLocationI.
FTHelper constructs the XxxxSubLocation variant of objects for
sub-locations of SplitLocations.

This would provide the functionality you want, provides for
self-contained objects, and retains a clean object interface. At least
IMHO.

A simpler solution would be to put parent_seq_id() into
Bio::LocationI, which has the disadvantage of urging all location
instances which are not sub-locations to provide a dummy value. 

What do you think? Jason, any comment?

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