Bio::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://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/

AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

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    :