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

package Bio::MUST::Core::Seq;
# ABSTRACT: Nucleotide or protein sequence
# CONTRIBUTOR: Catherine COLSON <ccolson@doct.uliege.be>
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@uliege.be>
$Bio::MUST::Core::Seq::VERSION = '0.252040';
use Moose;
use MooseX::SemiAffordanceAccessor;
use namespace::autoclean;

# use Smart::Comments '###';

use autodie;
use feature qw(say);

use Carp;

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:seqtypes :seqids :gaps);
use aliased 'Bio::MUST::Core::SeqId';

has 'seq_id' => (
    is       => 'rw',
    isa      => 'Bio::MUST::Core::SeqId',
    required => 1,
    coerce   => 1,
    handles  => qr{.*}xms,      # expose all SeqId methods (and attributes)
);


has 'seq' => (
    traits   => ['String'],
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Types::Seq',
    default  => q{},            # can be empty
    coerce   => 1,
    writer   => '_set_seq',
    handles  => {
            seq_len => 'length',
         append_seq => 'append',
        replace_seq => 'replace',
           edit_seq => 'substr',
    },
);



# TODO: check whether this could be done by some Moose extension

sub clone {
    my $self = shift;

    return $self->new(
        seq_id => $self->full_id, seq => $self->seq
    );
}


# boolean assertions
# TODO: optimize these assertions via caching


sub is_protein {
    my $self = shift;
    return 1 if $self->seq =~ $PROTLIKE;
    return 0;                               # at least 1 non-nt char
}