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Bio::Coordinate::ChainUser Contributed Perl DocumentaBio::Coordinate::Chain(3)

NAME
       Bio::Coordinate::Chain -	Mapping	locations through a chain of
       coordinate mappers.

VERSION
       version 1.007001

SYNOPSIS
	 # create Bio::Coordinate::Pairs, or any MapperIs, somehow
	 $pair1; $pair2;

	 # add them into a Chain
	 $collection = Bio::Coordinate::Chain->new;
	 $collection->add_mapper($pair1);
	 $collection->add_mapper($pair2);

	 # create a position and map it
	 $pos =	Bio::Location::Simple->new (-start => 5, -end => 9 );
	 $match	= $collection->map($pos);
	 if ($match) {
	     sprintf "Matches at %d-%d\n", $match->start, $match->end,
	 } else	{
	     print "No match\n";
	 }

DESCRIPTION
       This class assumes that you have	built several mappers and want to link
       them together so	that output from the previous mapper is	the next
       mappers input. This way you can build arbitrarily complex mappers from
       simpler components.

       Note that Chain does not	do any sanity checking on its mappers. You are
       solely responsible that input and output	coordinate systems, direction
       of mapping and parameters internal to mappers make sense	when chained
       together.

       To put it bluntly, the present class is just a glorified	foreach	loop
       over an array of	mappers	calling	the map	method.

       It would	be neat	to an internal function	that would generate a new
       single step mapper from those included in the chain. It should speed
       things up considerably. Any volunteers?

METHODS
   map
	Title	: map
	Usage	: $newpos = $obj->map($pos);
	Function: Map the location through all the mappers in the chain.
	Example	:
	Returns	: new Location in the output coordiante	system
	Args	: a Bio::Location::Simple object

   sort
       You do not really want to sort your chain, do you! This function	does
       nothing other than a warning.

   Inherited methods
   add_mapper
	Title	: add_mapper
	Usage	: $obj->add_mapper($mapper)
	Function: Pushes one Bio::Coodinate::MapperI into the list of mappers.
		  Sets _is_sorted() to false.
	Example	:
	Returns	: 1 when succeeds, 0 for failure.
	Args	: mapper object

   mappers
	Title	: mappers
	Usage	: $obj->mappers();
	Function: Returns or sets a list of mappers.
	Example	:
	Returns	: array	of mappers
	Args	: array	of mappers

   each_mapper
	Title	: each_mapper
	Usage	: $obj->each_mapper();
	Function: Returns a list of mappers.
	Example	:
	Returns	: array	of mappers
	Args	: none

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

   test
	Title	: test
	Usage	: $obj->test;
	Function: test that both components of all pairs are of	the same length.
		  Ran automatically.
	Example	:
	Returns	: boolean
	Args	:

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.

CONTRIBUTOR
       Ewan Birney <birney@ebi.ac.uk>

perl v5.32.1			  2016-12-15	     Bio::Coordinate::Chain(3)

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

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