[Bioperl-l] Split locations

Hilmar Lapp hilmarl@yahoo.com
Sun, 29 Apr 2001 22:01:01 -0700

Elia Stupka wrote:
> I have changed the sub_Location method on split locations. It used to
> order locations even if the order parameter was not defined. This screwed
> EMBL/Genbank dumping majorly because if an mRNA was defined as being made
> of 300..400 on accession A and then 30..70 on the sequence itself (master
> seq), the order was reversed. Why is the ordering necessary at all? Is it
> just for the min_start and max_start methods to work?

More or less, yes. min_start() for SplitLocationI implementors is
supposed to return the minimum start position among its
sublocations (but obviously only among those on the same
sequence!), and the other min/max methods respectively. The
present implementation expects the sublocations to be sorted in
order to avoid a sort on every call to min/max_something. Right,
Jason? I'm actually not even sure it handles remote locations
properly, I have to check.

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