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

Hilmar Lapp hilmarl@yahoo.com
Mon, 30 Apr 2001 10:08:29 -0700

Elia Stupka wrote:
> > I think ->is_remote is useful, otherwise you have to carry around your
> > parent seqid everywhere.
> Yes, let me just defend my commin on this one ;) is_remote is just a nice
> way in systems like bioperl-db, where we have a series of DBAdaptors for
> each object we store. In this case you would really have to carry the
> original seqid down a few adaptors (seq->feature->location), just to do an
> if statement to see if it's remote or not.

This was my feeling: the utility of this method is tied to some
quite specific application and not intuitive anywhere else (a
Location object should really be self-contained, and then
is_remote() doesn't make sense any more). Normally, this would be
the situation in which you roll your own implementation and/or
derive from the core class. I suspect this is difficult in your
case because you may be using FTHelper, which has the
to-be-created objects types hard-coded. Is this the case?

Note that in general you can't even rely on this method being
present because it's not in the interface (Bio::LocationI). The
idea of putting it into the interface makes me even unhappier.

Hilmar Lapp                              email: hilmarl@yahoo.com
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757