File Coverage

blib/lib/GenOO/RegionCollection/Factory/BED.pm

Criterion	Covered	Total	%
statement	18	18	100.0
branch	2	2	100.0
condition			n/a
subroutine	5	5	100.0
pod	0	1	0.0
total	25	26	96.1

# POD documentation - main docs before the code

=head1 NAME

GenOO::RegionCollection::Factory::BED - Factory for creating GenOO::RegionCollection object from a BED file

=head1 SYNOPSIS

    # Creates GenOO::RegionCollection object from a BED file

    # Preferably use it through the generic GenOO::RegionCollection::Factory
    my $factory = GenOO::RegionCollection::Factory->create('BED',
        {
            file => 'sample.bed'
        }
    );

=head1 DESCRIPTION

    An instance of this class is a concrete factory for the creation of a
    L<GenOO::RegionCollection> object from a BED file. It offers the method
    "read_collection" (as the consumed role requires) which returns the actual
    L<GenOO::RegionCollection> object in the form of
    L<GenOO::RegionCollection::Type::DoubleHashArray>. The latter is the implementation
    of the L<GenOO::RegionCollection> class based on the complex data structure
    L<GenOO::Data::Structure::DoubleHashArray>.

=head1 EXAMPLES

    # Create a concrete factory
    my $factory_implementation = GenOO::RegionCollection::Factory->create('BED',
        {
            file => 'sample.bed'
        }
    );

    # Return the actual GenOO::RegionCollection object
    my $collection = $factory_implementation->read_collection;
    print ref($collection) # GenOO::RegionCollection::Type::DoubleHashArray

=cut

# Let the code begin...

package GenOO::RegionCollection::Factory::BED;
$GenOO::RegionCollection::Factory::BED::VERSION = '1.5.1';

#######################################################################
#######################   Load External modules   #####################
#######################################################################
use Moose;
use namespace::autoclean;


#######################################################################
#########################   Load GenOO modules   ######################
#######################################################################
use GenOO::RegionCollection::Type::DoubleHashArray;
use GenOO::Data::File::BED;


#######################################################################
#######################   Interface attributes   ######################
#######################################################################
has 'file' => (
	isa      => 'Str',
	is       => 'ro',
	required => 1
);

has 'redirect_score_to_copy_number' => (
      traits  => ['Bool'],
      is      => 'rw',
      isa     => 'Bool',
      default => 0,
      lazy    => 1
);

has 'filter_code' => (
	isa      => 'CodeRef',
	is       => 'ro',
	default  => sub { sub {return 1} }
);


#######################################################################
##########################   Consumed roles   #########################
#######################################################################
with 'GenOO::RegionCollection::Factory::Requires';


#######################################################################
########################   Interface Methods   ########################
#######################################################################
sub read_collection {
	my ($self) = @_;

	my $collection = GenOO::RegionCollection::Type::DoubleHashArray->new;

	my $parser = GenOO::Data::File::BED->new(
		file                          => $self->file,
		redirect_score_to_copy_number => $self->redirect_score_to_copy_number,
	);

	while (my $record = $parser->next_record) {
		$collection->add_record($record) if $self->filter_code->($record);
	}

	return $collection;
}

1;