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

use Carp;
use Smart::Comments -ENV;
use List::AllUtils qw/max pairmap indexes/;
use Modern::Perl;

use Bio::MUST::Core 0.180230;
use Bio::MUST::Core::Constants qw(:gaps :files);
use aliased 'Bio::MUST::Core::SeqMask';
use aliased 'Bio::MUST::Core::Seq';

####### [PROCESS] Value of env verbosity : scalar(split ' ', $ENV{Smart_Comments})

# ATTRIBUTES

has 'seq' => (
    is          => 'ro',
    isa         => 'Bio::MUST::Core::Seq',
    required    => 1,
);

has 'score' => (
    is          => 'ro',
    isa         => 'Str',
    required    => 1,
);

has 'nogap_seq' => (
    is          => 'ro',
    isa         => 'Bio::MUST::Core::Seq',
    lazy        => 1,
    builder     => '_build_nogap_seq',
);

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

has 'delchar' => (
    is            => 'ro',
    isa            => 'Str',
    default        => ' ',
);

has 'nogap_shifts' => (
    is          => 'ro',
    isa         => 'ArrayRef[Int]', # Future 'Bio::MUST::Core::SeqMask' or not
    lazy        => 1,
    writer      => '_set_nogap_shifts',
    builder     => '_build_nogap_shifts',
);

has 'shifts' => (
    is          => 'ro',
    isa         => 'ArrayRef[Int]', # Future 'Bio::MUST::Core::SeqMask' or not
    lazy        => 1,
    writer      => '_set_shifts',