———#
# BioPerl module for FAST::Bio::SeqFeature::Gene::NC_Feature.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by David Block <dblock@gene.pbi.nrc.ca>
#
# Copyright David Block
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::SeqFeature::Gene::NC_Feature.pm - superclass for non-coding features
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
=head1 AUTHOR - David Block
Email dblock@gnf.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
use
strict;
# Object preamble - inherits from FAST::Bio::Root::Root
sub
new {
my
(
$class
,
@args
) =
@_
;
my
$self
=
$class
->SUPER::new(
@args
);
my
(
$is_coding
) =
$self
->_rearrange([
qw(IS_CODING)
],
@args
);
# default is non-coding
$self
->is_coding(
defined
(
$is_coding
) ?
$is_coding
: 0);
return
$self
;
}
=head2 is_coding
Title : is_coding
Usage : if ($feature->is_coding()) {
#do something
}
Function: Whether or not the feature codes for amino acid.
Returns : FALSE
Args : none
=cut
sub
is_coding{
my
$self
=
shift
;
return
$self
->{
'is_coding'
} =
shift
if
@_
;
return
$self
->{
'is_coding'
};
}
=head2 cds
Title : cds
Usage : $cds=$feature->cds();
Function: get the coding sequence of this feature
Returns : undef
Args : none
=cut
sub
cds {
my
(
$self
,
@args
) =
@_
;
return
;
}
1;