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Bio::Coordinate::ExtraUsertContributed PeBio::Coordinate::ExtrapolatingPair(3)

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

VERSION
       version 1.007001

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.

METHODS
   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

INTERNAL METHODS
   _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

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 list.  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 of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 https://github.com/bioperl/%%7Bdist%7D

AUTHOR
       Heikki Lehvaslaiho <heikki@bioperl.org>

COPYRIGHT
       This software is	copyright (c) by Heikki	Lehvaslaiho.

       This software is	available under	the same terms as the perl 5
       programming language system itself.

perl v5.32.1			  2016-12Bio::Coordinate::ExtrapolatingPair(3)

NAME | VERSION | SYNOPSIS | DESCRIPTION | METHODS | INTERNAL METHODS | FEEDBACK | AUTHOR | COPYRIGHT

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