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Bio::Coordinate::Pair(User Contributed Perl DocumentatBio::Coordinate::Pair(3)

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

VERSION
       version 1.007001

SYNOPSIS
	 use Bio::Location::Simple;
	 use Bio::Coordinate::Pair;

	 my $match1 = Bio::Location::Simple->new
	     (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
	 my $match2 = Bio::Location::Simple->new
	     (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1	);
	 my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					       -out => $match2
					       );
	 # location to match
	 $pos =	Bio::Location::Simple->new
	     (-start =>	25, -end => 25,	-strand=> -1 );

	 # results are in a Bio::Coordinate::Result
	 # they	can be Matches and Gaps; are  Bio::LocationIs
	 $res =	$pair->map($pos);
	 $res->isa('Bio::Coordinate::Result');
	 $res->each_match == 1;
	 $res->each_gap	== 0;
	 $res->each_Location ==	1;
	 $res->match->start == 5;
	 $res->match->end == 5;
	 $res->match->strand ==	-1;
	 $res->match->seq_id eq	'peptide';

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.

       The map() method	returns	Bio::Coordinate::Results with
       Bio::Coordinate::Result::Gaps. The calling code have to deal (process
       or ignore) them.

METHODS
   new
   in
	Title	: in
	Usage	: $obj->in('peptide');
	Function: Set and read the input coordinate system.
	Example	:
	Returns	: value	of input system
	Args	: new value (optional),	Bio::LocationI

   out
	Title	: out
	Usage	: $obj->out('peptide');
	Function: Set and read the output coordinate system.
	Example	:
	Returns	: value	of output system
	Args	: new value (optional),	Bio::LocationI

   swap
	Title	: swap
	Usage	: $obj->swap;
	Function: Swap the direction of	mapping; input <-> output
	Example	:
	Returns	: 1
	Args	:

   strand
	Title	: strand
	Usage	: $obj->strand;
	Function: Get strand value for the pair
	Example	:
	Returns	: ( 1 |	0 | -1 )
	Args	:

   test
	Title	: test
	Usage	: $obj->test;
	Function: test that both components are	of the same length
	Example	:
	Returns	: ( 1 |	undef )
	Args	:

   map
	Title	: map
	Usage	: $newpos = $obj->map($pos);
	Function: Map the location from	the input coordinate system
		  to a new value in the	output coordinate system.
	Example	:
	Returns	: new Bio::LocationI in	the output coordinate system or	undef
	Args	: Bio::LocationI object

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			  2016-12-15	      Bio::Coordinate::Pair(3)

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

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