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lib/Bio/RNA/Barriers/RateMatrix.pm  view on Meta::CPAN

package Bio::RNA::Barriers::RateMatrix;
our $VERSION = '0.03';

use 5.012;
use strict;
use warnings;

use Moose;
use MooseX::StrictConstructor;
use namespace::autoclean;
use Moose::Util::TypeConstraints qw(enum subtype as where message);

use autodie qw(:all);
use overload '""' => \&stringify;
use Scalar::Util qw( reftype looks_like_number );
use List::Util qw( all uniqnum );

enum __PACKAGE__ . 'RateMatrixType', [qw(TXT BIN)];

# Natural number type directly from the Moose docs.
subtype 'PosInt',
    as 'Int',
    where { $_ > 0 },
    message { "The number you provided, $_, was not a positive number" };

has 'file_name' => (
    is        => 'ro',
    isa       => 'Str',
    predicate => 'has_file_name',
);
has 'file_type' => (
    is       => 'rw',
    isa      => __PACKAGE__ . 'RateMatrixType',
    required => 1,
);
has '_file_handle' => (
    is       => 'ro',
    isa      => 'FileHandle',
    init_arg => 'file_handle',
    lazy     => 1,
    builder  => '_build_file_handle',
);
# Splice rate matrix directly when reading the data. This can read big
# matrices when only keeping a few entries.
has 'splice_on_parsing' => (
    is        => 'ro',
    isa       => 'ArrayRef[PosInt]',
    predicate => 'was_spliced_on_parsing',
);
has '_data' => (is => 'ro', lazy => 1, builder => '_build_data');

sub BUILD {
    my $self = shift;

    # Enforce data is read from handle immediately despite laziness.
    $self->dim;
}

# Read the actual rate data from the input file and construct the
# matrix from it.
sub _build_data {
    my $self = shift;

    my $rate_matrix;
    if ($self->file_type eq 'TXT') {
        $rate_matrix = __PACKAGE__->read_text_rate_matrix(
            $self->_file_handle,
            $self->splice_on_parsing,
        );
    }