NAME

Bio::LocatableSeq - A Sequence object with start/end points on it

SYNOPSIS

    # 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);

DESCRIPTION

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.

CONTACT

Ewan Birney <birney@ebi.ac.uk>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

start

 Title   : start
 Usage   : $obj->start($newval)
 Function: 
 Returns : value of start
 Args    : newvalue (optional)

end

 Title   : end
 Usage   : $obj->end($newval)
 Function: 
 Returns : value of end
 Args    : newvalue (optional)

strand

 Title   : strand
 Usage   : $obj->strand($newval)
 Function: 
 Returns : value of strand
 Args    : newvalue (optional)

get_nse

 Title   : get_nse
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :