Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets
use Bio::Location::Simple; use Bio::Coordinate::ExtrapolatingPair;
$match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
$pair = Bio::Coordinate::ExtrapolatingPair->
new(-in => $match1,
-out => $match2,
-strict => 1
);
$pos = Bio::Location::Simple->new
(-start => 40, -end => 60, -strand=> 1 );
$res = $pair->map($pos);
$res->start eq 20;
$res->end eq 20;
This class represents a one continuous match between two coordinate systems represented by Bio::Location::Simple objects. The relationship is directed and reversible. It implements methods to ensure internal consistency, and map continuous and split locations from one coordinate system to another.
This class is an elaboration of Bio::Coordoinate::Pair. The map
function returns only matches which is the mode needed most of
tehtime. By default the matching regions between coordinate systems
are boundless, so that you can say e.g. that gene starts from here in
the chromosomal coordinate system and extends indefinetely in both
directions. If you want to define the matching regions exactly, you
can do that and set strict() to true.
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Email: heikki@ebi.ac.uk Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : strict Usage : $obj->strict(1); Function: Set and read the strictness of the coordinate system. Example : Returns : value of input system Args : boolean
Title : map
Usage : $newpos = $obj->map($loc);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
In extrapolating coodinate system there is no location zero.
Locations are...
Example :
Returns : new location in the output coordinate system or undef
Args : Bio::Location::Simple
Title : _map
Usage : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called
multiple times by map() if the location to be mapped is a
split location
Example : Returns : new location in the output coordinate system or undef Args : Bio::Location::Simple