SYNOPSIS¶
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;
DESCRIPTION¶
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::Coordinate::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.
new¶
strict¶
Title : strict
Usage : $obj->strict(1);
Function: Set and read the strictness of the coordinate system.
Example :
Returns : value of input system
Args : boolean
map¶
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
_map¶
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