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

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

use Data::UUID;
use List::AllUtils qw(each_array);

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


# private attributes

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

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

# public attributes

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

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

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;
    }
);

has 'gene_begin' => (
    is       => 'ro',
    isa      => 'Num',
    init_arg => undef,
    default  => 1,
);

has 'gene_end' => (