Provided by: libbio-perl-perl_1.6.923-1_all bug


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


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

         # add them into a Chain
         $collection = Bio::Coordinate::Chain->new;

         # 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";


       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?


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AUTHOR - Heikki Lehvaslaiho

       Email:  heikki-at-bioperl-dot-org


       Ewan Birney,


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

        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
        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

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

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

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

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