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; $collection->add_mapper($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"; } 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?

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom Ewan Birney, birney@ebi.ac.uk 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 :