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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

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?

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:

	 http://bugzilla.open-bio.org/

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

CONTRIBUTORS
       Ewan Birney, birney@ebi.ac.uk

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

   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

   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	:

perl v5.14.1			  2011-07-22	     Bio::Coordinate::Chain(3)
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