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>