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package Bio::Coordinate::Chain;
our $AUTHORITY = 'cpan:BIOPERLML';
$Bio::Coordinate::Chain::VERSION = '1.007001';
use utf8;
use strict;
use warnings;
use Bio::Root::Root;
use Bio::Coordinate::Result;
use parent qw(Bio::Coordinate::Collection Bio::Coordinate::MapperI);
# ABSTRACT: Mapping locations through a chain of coordinate mappers.
# AUTHOR: Heikki Lehvaslaiho <heikki@bioperl.org>
# OWNER: Heikki Lehvaslaiho
# LICENSE: Perl_5
# CONTRIBUTOR: Ewan Birney <birney@ebi.ac.uk>
sub map {
my ($self,$value) = @_;
$self->throw("Need to pass me a value.")
unless defined $value;
$self->throw("I need a Bio::Location, not [$value]")
unless $value->isa('Bio::LocationI');
$self->throw("No coordinate mappers!")
unless $self->each_mapper;
my $res = Bio::Coordinate::Result->new();
foreach my $mapper ($self->each_mapper) {
my $res = $mapper->map($value);
return unless $res->each_match;
$value = $res->match;
}
return $value;
}
sub sort{
my ($self) = @_;
$self->warn("You do not really want to sort your chain, do you!\nDoing nothing.");
}
1;
__END__
=pod
=encoding utf-8
=head1 NAME
Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers.
=head1 VERSION
version 1.007001
=head1 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";
}
=head1 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?
=head1 METHODS
=head2 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
=head2 sort
You do not really want to sort your chain, do you! This function does nothing
other than a warning.
=head2 Inherited methods
=head2 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
=head2 mappers
Title : mappers
Usage : $obj->mappers();
Function: Returns or sets a list of mappers.
Example :
Returns : array of mappers
Args : array of mappers
=head2 each_mapper
Title : each_mapper
Usage : $obj->each_mapper();
Function: Returns a list of mappers.
Example :
Returns : array of mappers
Args : none
=head2 swap
Title : swap
Usage : $obj->swap;
Function: Swap the direction of mapping;input <-> output
Example :
Returns : 1
Args :
=head2 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 :
=head1 FEEDBACK
=head2 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 list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting bugs
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
=head1 AUTHOR
Heikki Lehvaslaiho <heikki@bioperl.org>
=head1 COPYRIGHT
This software is copyright (c) by Heikki Lehvaslaiho.
This software is available under the same terms as the perl 5 programming language system itself.
=head1 CONTRIBUTOR
=for stopwords Ewan Birney
Ewan Birney <birney@ebi.ac.uk>
=cut
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