Bio::Coordinate::ExtrapolatingPair(3) 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::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.


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AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org


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