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

package Bio::MUST::Core::Ali::Temporary;
# ABSTRACT: Thin wrapper for a temporary mapped Ali written on disk
$Bio::MUST::Core::Ali::Temporary::VERSION = '0.252040';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Path::Class qw(file);

use Bio::MUST::Core::Types;

# Note: tried to implement it as a subclass of Bio::MUST::Core::Ali but this
# led to issues: (1) coercions became a nightmare and (2) the temp_fasta was
# written as soon as the Ali was created and thus was empty

# TODO: allows to specify the directory for the temp file (File::Temp tmpdir)
# TODO: allows to specify a template for the temp file name?

# ATTRIBUTES


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


has 'args' => (
    is       => 'ro',
    isa      => 'HashRef',
    lazy     => 1,
    builder  => '_build_args',
);


has 'file' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Types::File',
    init_arg => undef,
    coerce   => 1,
    writer   => '_set_file',
    handles  => {
        remove   => 'remove',
        filename => 'stringify',
    },
);


has 'mapper' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdMapper',
    init_arg => undef,
    writer   => '_set_mapper',
    handles  => [ qw(all_long_ids all_abbr_ids long_id_for abbr_id_for) ],