$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;
DESCRIPTIONThis 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.
Mailing ListsUser feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportPlease direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugsreport bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
AUTHOR - Heikki LehvaslaihoEmail: heikki-at-bioperl-dot-org
APPENDIXThe 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