Bio::Coordinate::Chain(3pm) User Contributed Perl Documentation Bio::Coordinate::Chain(3pm)
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
", $match->start, $match->end,
} else {
print "No match
";
}
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://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 the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
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 :
perl v5.14.2 2012-03-02 Bio::Coordinate::Chain(3pm)