——package
Bio::CUA::CUB;
use
5.006;
use
strict;
use
warnings;
=head1 NAME
Bio::CUA::CUB - This is the parent class for all classs processing
codon usage bias (CUB).
=head1 SYNOPSIS
At present, this class largely inherits from
L<Bio::CUA::Summarizer>. The class may be updated in future depending
on the needs of new analyses.
Please refer to its child classes L<Bio::CUA::CUB::Builder> and
L<Bio::CUA::CUB::Calculator> for usage of methods.
=head1 METHODS
=head2 no_atg
Title : no_atg
Usage : $status = $self->no_atg([$newVal])
Function: get/set the status whether ATG should be excluded in tAI
calculation.
Returns : current status after updating
Args : optional. 1 for true, 0 for false
=cut
sub
no_atg
{
my
(
$self
,
$val
) =
@_
;
$self
->set_tag(
'no_atg'
,
$val
)
if
(
defined
(
$val
));
return
$self
->get_tag(
'no_atg'
);
}
=head1 AUTHOR
Zhenguo Zhang, C<< <zhangz.sci at gmail.com> >>
=head1 BUGS
Please report any bugs or feature requests to C<bug-bio-cua at rt.cpan.org>, or through
the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-CUA>. I will be notified, and then you'll
automatically be notified of progress on your bug as I make changes.
=head1 SUPPORT
You can find documentation for this class with the perldoc command.
perldoc Bio::CUA::CUB
You can also look for information at:
=over 4
=item * RT: CPAN's request tracker (report bugs here)
=item * AnnoCPAN: Annotated CPAN documentation
=item * CPAN Ratings
=item * Search CPAN
=back
=head1 ACKNOWLEDGEMENTS
=head1 LICENSE AND COPYRIGHT
Copyright 2015 Zhenguo Zhang.
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 L<http://www.gnu.org/licenses/>.
=cut
1;
# End of Bio::CUA::CUB