Bio-RNA-Treekin

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Changes  view on Meta::CPAN

        Added LICENSE file to MANIFEST.

0.04    2022-12-08
        - added Perl v5.14 requirement to the distribution meta data
        - added GPLv3 LICENSE file

0.03    2022-01-13
        - removed debug output spamming the terminal when reading a file

0.02    2022-01-03
        - added support for '# of iterations' footer in new Treekin versions

0.01    2021-12-22
        First version, released on an unsuspecting world.

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

               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;
}

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

        'States limit'    => $self->states_limit,
    );

    my $header_str = join "\n", pairmap { "# $a: $b" } @header_entries;

    # Population data
    my $population_str
        = join "\n", map { "$_" } @{ $self->_population_data };

    # Footer (new Treekin versions only).
    my $footer_str = $self->has_of_iterations
                     ? '# of iterations: ' . $self->of_iterations
                     : q{};

    my $self_as_str  = $header_str . "\n" . $population_str;
    $self_as_str    .= "\n" . $footer_str if $footer_str;

    return $self_as_str;
}

__PACKAGE__->meta->make_immutable;

t/data/treekin_single_small_new.kin  view on Meta::CPAN

1.00000000000000005551e-01 9.975614e-01 1.780033e-03 1.699285e-04 4.366637e-04 2.853783e-05 1.732678e-05 5.203420e-06 2.284726e-07 7.195039e-07
3.29999999999999960032e-01 9.925545e-01 5.493689e-03 5.726556e-04 1.206952e-03 9.145588e-05 5.531990e-05 1.686918e-05 2.355482e-06 6.251624e-06 
8.58999999999999874767e-01 9.835173e-01 1.233819e-02 1.520550e-03 2.184748e-03 2.229225e-04 1.337191e-04 4.220111e-05 1.405266e-05 2.627692e-05 
2.07569999999999943441e+00 9.707329e-01 2.190646e-02 3.592723e-03 2.808839e-03 4.666975e-04 2.750026e-04 9.350034e-05 6.143765e-05 6.249221e-05 
4.87410999999999816623e+00 9.586998e-01 2.924071e-02 7.377603e-03 2.945105e-03 8.148683e-04 4.643097e-04 1.828670e-04 1.859488e-04 8.880556e-05 
1.13104529999999954271e+01 9.513184e-01 3.080657e-02 1.240492e-02 3.020511e-03 1.099316e-03 5.992051e-04 2.952576e-04 3.610896e-04 9.469268e-05 
2.61140418999999894822e+01 9.475712e-01 3.071786e-02 1.589999e-02 3.076343e-03 1.171927e-03 6.248600e-04 3.656116e-04 4.772013e-04 9.499057e-05 
6.01622963699999715459e+01 9.468848e-01 3.069401e-02 1.656599e-02 3.087073e-03 1.172795e-03 6.246081e-04 3.765550e-04 4.991709e-04 9.502509e-05 
1.38473281650999922476e+02 9.468742e-01 3.069365e-02 1.657630e-02 3.087240e-03 1.172769e-03 6.245952e-04 3.766629e-04 4.995109e-04 9.502564e-05 
1.00000000000000000000e+12 9.468742e-01 3.069365e-02 1.657630e-02 3.087240e-03 1.172769e-03 6.245952e-04 3.766629e-04 4.995109e-04 9.502564e-05 
# of iterations: 9