File Coverage

blib/lib/Bio/Coordinate/Chain.pm

Criterion	Covered	Total	%
statement	28	30	93.3
branch	4	8	50.0
condition			n/a
subroutine	7	8	87.5
pod	2	2	100.0
total	41	48	85.4

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
# OWNER:    Heikki Lehvaslaiho
# LICENSE:  Perl_5

# CONTRIBUTOR: Ewan Birney



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__