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Bio-RNA-Treekin-0.05
River stage zero No dependents
++
/ Bio::RNA::Treekin::PopulationDataRecord

NAME

Bio::RNA::Treekin::PopulationDataRecord - Parse, query, and manipulate a single data line from a Treekin file.

SYNOPSIS

    use Bio::RNA::Treekin;

    my $pop_data = Bio::RNA::Treekin::PopulationDataRecord->new(
                    '<single population data line from Treekin file>');

    print "Populations at time", $pop_data->time, ":\n";
    print "    min $_: ", $pop_data->of_min($_), "\n"
        for 1..$pop_data->min_count;

    my @big_pops = grep {$pop_data->of_min($_) > 0.1} 1..$pop_data->min_count;
    print 'Minima ', join(q{, }, @big_pops), ' have a population greater 0.1\n';

DESCRIPTION

This class provides a population data record that stores the information from a single data line of a Treekin file.

METHODS

Bio::RNA::Treekin::PopulationDataRecord->new($treekin_file_line)

Construct a new population data record from a single data line of a Treekin file.

Bio::RNA::Treekin::PopulationDataRecord->new(arg => $argval, ...)

Construct a new population data record.

Required arguments:
time

The point in time that the population data describes.

populations

Array ref of the population values for all minima.

$pop_data->min_count

Return the number of minima in this data record. This count is not stored explicitely, but inferred from the number of populations supplied during construction.

$pop_data->time

Return the point in time (in arbitrary time units) that the population data describes.

$pop_data->clone

Return a deep copy of this data record.

$pop_data->set_min_count($new_min_count)

Increase the number of minima to $new_min_count. The newly added minima will have population values of 0.

Currently, the number of minima cannot be decreased to avoid data loss.

$pop_data->populations

Return a list of all population values for minima 1, 2, ..., n in this ordner.

$pop_data->of_min($minimum)

Return the population value of the given $minimum at the time of this record.

$pop_data->transform($maps_to_min_ref, $new_min_count)

Transform (reorder and resize) the population data according to a given mapping ($maps_to_min_ref) and resize to a given number of minima ($new_min_count). All minima that are not mapped to a new position are discarded (replaced by zero).

NOTE: Ensure that no two minima are mapped to the same position or crap will happen.

Arguments:
$maps_to_min_ref:

Hash ref that specifies for each kept minimum (key) to which new minimum (value) it is supposed to be mapped.

$new_min_count:

New size (number of mins) of the record after the transformation. Defaults to the maximum value of $maps_to_min_ref.

$pop_data->stringify

"$pop_data"

Convert this data record into a string representation, corresponding to a single line as found in a Treekin file.

AUTHOR

Felix Kuehnl, <felix@bioinf.uni-leipzig.de>

BUGS

Please report any bugs or feature requests by raising an issue at https://github.com/xileF1337/Bio-RNA-Treekin/issues.

You can also do so by mailing to bug-bio-rna-treekin at rt.cpan.org, or through the web interface at https://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-RNA-Treekin. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Bio::RNA::Treekin

You can also look for information at:

LICENSE AND COPYRIGHT

Copyright 2019-2021 Felix Kuehnl.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.