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lib/Bio/MUST/Core/Ali/Stash.pm  view on Meta::CPAN

package Bio::MUST::Core::Ali::Stash;
# ABSTRACT: Thin wrapper for an indexed Ali read from disk
$Bio::MUST::Core::Ali::Stash::VERSION = '0.252040';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments;

use Carp;

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:seqids);
use aliased 'Bio::MUST::Core::Ali';

# ATTRIBUTES


has 'seqs' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    required => 1,
    handles  => [
        qw(filename count_comments all_comments get_comment
            guessing all_seq_ids has_uniq_ids is_protein is_aligned
            get_seq first_seq all_seqs filter_seqs count_seqs
            gapmiss_regex
        )
    ],      # comment-related methods needed by IdList
);


has 'lookup' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdList',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_lookup',
    handles  => [ qw(index_for) ],
);

with 'Bio::MUST::Core::Roles::Aliable';

## no critic (ProhibitUnusedPrivateSubroutines)

sub _build_lookup {
    return shift->seqs->new_lookup;
}

## use critic

# ACCESSORS


sub get_seq_with_id {
    my $self = shift;
    my $id   = shift;

    # override Ali method with faster lookup-based alternative
    my $index = $self->index_for($id);
    return $self->get_seq($index)
        if defined $index;