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lib/Bio/MUST/Apps/HmmCleaner.pm  view on Meta::CPAN

package Bio::MUST::Apps::HmmCleaner;
# ABSTRACT: Main class for HmmCleaner
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>
$Bio::MUST::Apps::HmmCleaner::VERSION = '0.243280';
use Moose;
use namespace::autoclean;

use Smart::Comments -ENV;
use List::AllUtils qw/uniq max/;
use Modern::Perl;

use Carp;
use Path::Class;

use Bio::MUST::Core 0.180230;
use Bio::MUST::Core::Constants qw(:gaps :files);
use Bio::MUST::Drivers 0.180270;
use Bio::MUST::Drivers::Hmmer::Model::Temporary;

use aliased 'Bio::MUST::Core::Seq';
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdList';

use aliased 'Bio::MUST::Apps::HmmCleaner::Process';
use aliased 'Bio::MUST::Apps::HmmCleaner::Cleaner';

# ATTRIBUTES

has 'ali' => (
    is            => 'ro',
    isa            => 'Bio::MUST::Core::Ali',
    required    => 1,
    coerce        => 1,
);

has 'ali_model' => (
    is          => 'ro',
    isa         => 'Bio::MUST::Core::Ali',
    required    => 1,
    coerce      => 1,
);

has 'threshold' => (
    is          => 'ro',
    isa         => 'Int',
    required    => 1,
    writer      => '_set_threshold',
    default     => 1,
);

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

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

has 'symfrac' => (
    is          => 'ro',
    isa         => 'Num',
    default     => 0.5,