| Bio::Coordinate::Chain(3pm) | User Contributed Perl Documentation | Bio::Coordinate::Chain(3pm) |
Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers.
version 1.007001
# 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?
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
You do not really want to sort your chain, do you! This function does nothing other than a warning.
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 :
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 list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/%%7Bdist%7D
Heikki Lehvaslaiho <heikki@bioperl.org>
This software is copyright (c) by Heikki Lehvaslaiho.
This software is available under the same terms as the perl 5 programming language system itself.
Ewan Birney <birney@ebi.ac.uk>
| 2020-11-24 | perl v5.32.0 |