Bio::Coordinate::ExtrapolatingPair(3pm) 		User Contributed Perl Documentation		   Bio::Coordinate::ExtrapolatingPair(3pm)

NAME

       Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets

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.

FEEDBACK

   Mailing Lists
       User 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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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 Bugs
       report 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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

APPENDIX

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

   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

perl v5.14.2							    2012-03-02				   Bio::Coordinate::ExtrapolatingPair(3pm)