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

package Bio::MUST::Core::IdMapper;
# ABSTRACT: Id mapper for translating sequence ids
$Bio::MUST::Core::IdMapper::VERSION = '0.252040';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Carp;
use List::AllUtils qw(mesh uniq each_array);

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:files);
use aliased 'Bio::MUST::Core::SeqId';
with 'Bio::MUST::Core::Roles::Commentable';


# long_ids and abbr_ids public arrays
has $_ . '_ids' => (
    traits   => ['Array'],
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Types::full_ids',
    default  => sub { [] },
    coerce   => 1,
    writer   => '_set_' . $_ . '_ids',
    handles  => {
        'count_' . $_ . '_ids' => 'count',
          'all_' . $_ . '_ids' => 'elements',
    },
) for qw(long abbr);


# _long_id_for and _abbr_id_for private hashes for faster mapping
has '_' . $_ . '_id_for' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[Str]',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_' . $_ . '_id_for',
    handles  => {
        $_ . '_id_for' => 'get',
    },
) for qw(long abbr);


# Note: mesh, uniq and co do not work with the 'elements' native trait,
# hence the option to coerce the public array refs in all the following subs

# Note: private hashes are not updated once (lazily) built

## no critic (ProhibitUnusedPrivateSubroutines)

# same note as in IdList.pm about SeqId objects

sub _build_long_id_for {
    my $self = shift;

    my @abbr_ids = map { $_->full_id } $self->all_abbr_seq_ids;
    my @long_ids = map { $_->full_id } $self->all_long_seq_ids;

    return { mesh @abbr_ids, @long_ids };
}