Bio::LocatableSeq - A Sequence object with start/end points on it
# a normal sequence object $locseq->seq(); $locseq->id(); # has start,end points $locseq->start(); $locseq->end(); # inheriets off RangeI, so range operations possible $locseq->overlaps($seqfeature);
The locatable sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this.
It is, to be honest, not well integrated with the rest of bioperl, for example, the ->trunc function does not return a LocatableSeq object, as some might have thought. There are all sorts of nasty gotcha's about interactions between coordinate systems when these sort of objects are used.
Please post to the guts list for more about this, or contact Ewan Birney.
Ewan Birney <email@example.com>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : start Usage : $obj->start($newval) Function: Returns : value of start Args : newvalue (optional)
Title : end Usage : $obj->end($newval) Function: Returns : value of end Args : newvalue (optional)
Title : strand Usage : $obj->strand($newval) Function: Returns : value of strand Args : newvalue (optional)
Title : get_nse Usage : Function: Example : Returns : Args :