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lib/Bio/Palantir/Refiner/ClusterPlus.pm  view on Meta::CPAN

package Bio::Palantir::Refiner::ClusterPlus;
# ABSTRACT: Refiner internal class for handling ClusterPlus objects
$Bio::Palantir::Refiner::ClusterPlus::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use Data::UUID;

use aliased 'Bio::Palantir::Refiner::GenePlus';


# private attributes

has '_cluster' => (
    is      => 'ro',
    isa     => 'Bio::Palantir::Parser::Cluster',
    handles => [qw(
        rank name type sequence
        genomic_prot_begin genomic_prot_end genomic_prot_size
        genomic_prot_coordinates genomic_dna_begin genomic_dna_end
        genomic_dna_size genomic_dna_coordinates 
    )],
);

has 'gap_filling' => (
    is      => 'ro',
    isa     => 'Bool',
    default => 1,
);

has 'undef_cleaning' => (
    is      => 'ro',
    isa     => 'Bool',
    default => 1,
);

has 'from_seq' => (
    is      => 'ro',
    isa     => 'Bool',
    default => 0,
);

has 'module_delineation' => (
    is      => 'ro',
    isa     => 'Str',
    default => 'substrate-selection',
);

has 'uui' => (
    is       => 'ro',
    isa      => 'Str',
    init_arg => undef,
    default  => sub {
        my $self = shift;
        my $ug = Data::UUID->new;
        my $uui = $ug->create_str;    
        return $uui;
    }
);


# public array(s) of composed objects


has 'genes' => (