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lib/Bio/RNA/Treekin/Record.pm  view on Meta::CPAN

# Bio/RNA/Treekin/Record.pm

# Stores a data from a single row of the Treekin file, i.e. the populations of
# all minima at a given time point.
package Bio::RNA::Treekin::Record;
our $VERSION = '0.05';

use v5.14;                          # required for non-destructive subst m///r
use strict;
use warnings;

use Moose;
use MooseX::StrictConstructor;
use namespace::autoclean;

use autodie qw(:all);
use Scalar::Util qw(reftype openhandle);
use List::Util qw(first pairmap max uniqnum all);
use Carp qw(croak);

use Bio::RNA::Treekin::PopulationDataRecord;

use overload '""' => \&stringify;


has '_population_data'  => (
    is       => 'ro',
    required => 1,
    init_arg => 'population_data',
);

has 'date'              => (is => 'ro', required => 1);
has 'sequence'          => (is => 'ro', required => 1);
has 'method'            => (is => 'ro', required => 1);
has 'start_time'        => (is => 'ro', required => 1);
has 'stop_time'         => (is => 'ro', required => 1);
has 'temperature'       => (is => 'ro', required => 1);
has 'basename'          => (is => 'ro', required => 1);
has 'time_increment'    => (is => 'ro', required => 1);
has 'degeneracy'        => (is => 'ro', required => 1);
has 'absorbing_state'   => (is => 'ro', required => 1);
has 'states_limit'      => (is => 'ro', required => 1);

# Add optional attributes including predicate.
has $_ => (
               is        => 'ro',
               required  => 0,
               predicate => "has_$_",
          )
    foreach qw(
                 info
                 init_population
                 rates_file
                 file_index
                 cmd
                 of_iterations
            );

# Get number of population data rows stored.
sub population_data_count {
    my ($self) = @_;

    my $data_count = @{ $self->_population_data };
    return $data_count;
}

# Number of states / minima in this simulation.
# Get number of mins in the first population record; it should be the
# same for all records.
sub min_count {
    my $self = shift;

    my $first_pop = $self->population(0);
    confess 'min_count: no population data present'