/ 
bioperl-1.2.2
/ Bio::Coordinate::Chain

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    :